Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-24 23:55 -0500 (Sat, 24 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4886
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4676
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/31HostnameOS / ArchCHECK
biodbNcbi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-01-24 09:55 -0500 (Sat, 24 Jan 2026)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_22
git_last_commit: dc1f90a
git_last_commit_date: 2025-10-29 11:15:40 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on merida1

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNcbi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
StartedAt: 2026-01-24 16:01:31 -0500 (Sat, 24 Jan 2026)
EndedAt: 2026-01-24 16:02:41 -0500 (Sat, 24 Jan 2026)
EllapsedTime: 70.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2026-01-24 16:02:28.499][biodb::testContext]
biodb.INFO [2026-01-24 16:02:28.503][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:28.504][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2026-01-24 16:02:28.506][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:28.507][biodb::testContext]
biodb.INFO [2026-01-24 16:02:28.513][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:28.515][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:28.523][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:28.524][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-24 16:02:28.526][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.530][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-24 16:02:28.555][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.560][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-24 16:02:28.561][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.566][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-24 16:02:28.567][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-24 16:02:28.568][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-24 16:02:28.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.573][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-24 16:02:28.574][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-24 16:02:28.575][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.580][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-24 16:02:28.581][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-24 16:02:28.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.586][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-24 16:02:28.587][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-24 16:02:28.588][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-24 16:02:28.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.593][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-24 16:02:28.594][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.599][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-24 16:02:28.600][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-24 16:02:28.602][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-24 16:02:28.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.606][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:28.607][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-24 16:02:28.609][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-24 16:02:28.610][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-24 16:02:28.611][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-24 16:02:28.613][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-24 16:02:28.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.617][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-24 16:02:28.618][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-24 16:02:28.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.623][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-24 16:02:28.624][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-24 16:02:28.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.629][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-24 16:02:28.630][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-24 16:02:28.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.635][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-24 16:02:28.636][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-24 16:02:28.637][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-24 16:02:28.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.642][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:28.643][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-24 16:02:28.654][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-24 16:02:28.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.659][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-24 16:02:28.660][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-24 16:02:28.662][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-24 16:02:28.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.669][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-24 16:02:28.717][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.739][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-24 16:02:28.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:28.743][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.745][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.747][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.748][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:28.750][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:28.751][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.752][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-24 16:02:28.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:28.755][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.757][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:28.757][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:28.757][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:28.757][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:28.757][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:28.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:28.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.763][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:28.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.767][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.769][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:28.770][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:28.771][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.773][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.774][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-24 16:02:28.776][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.778][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:28.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:28.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.783][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.784][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.785][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.787][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:28.788][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:28.789][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.790][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-24 16:02:28.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:28.793][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.794][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.796][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:28.796][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:28.796][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:28.796][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:28.796][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:28.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:28.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:28.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.804][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.805][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:28.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:28.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.810][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.812][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-24 16:02:28.814][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.815][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-24 16:02:28.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:28.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.824][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:28.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:28.827][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.828][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-24 16:02:28.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:28.830][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.833][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.834][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:28.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:28.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.842][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:28.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:28.846][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.848][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.849][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-24 16:02:28.851][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.852][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:28.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:28.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.860][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.861][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:28.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:28.864][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.865][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-24 16:02:28.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:28.868][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:28.870][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:28.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:28.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:28.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:28.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:28.880][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:28.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:28.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:28.885][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:28.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:28.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:28.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:28.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:28.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:28.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:28.988][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-24 16:02:28.993][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-24 16:02:28.995][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-24 16:02:28.997][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-24 16:02:28.998][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-24 16:02:29.000][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:29.002][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:29.004][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:29.005][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-24 16:02:29.007][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:29.009][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:29.011][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-24 16:02:29.012][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:29.014][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:29.016][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:29.017][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:29.019][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-24 16:02:29.021][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-24 16:02:29.023][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-24 16:02:29.024][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-24 16:02:29.026][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-24 16:02:29.028][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-24 16:02:29.030][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-24 16:02:29.032][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-24 16:02:29.033][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-24 16:02:29.035][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-24 16:02:29.037][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-24 16:02:29.039][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-24 16:02:29.040][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-24 16:02:29.042][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-24 16:02:29.044][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-24 16:02:29.046][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-24 16:02:29.047][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-24 16:02:29.049][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-24 16:02:29.051][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-24 16:02:29.052][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-24 16:02:29.054][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-24 16:02:29.056][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-24 16:02:29.058][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-24 16:02:29.060][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-24 16:02:29.061][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-24 16:02:29.063][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-24 16:02:29.065][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-24 16:02:29.067][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-24 16:02:29.069][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-24 16:02:29.070][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:29.072][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-24 16:02:29.074][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-24 16:02:29.076][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-24 16:02:29.078][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-24 16:02:29.079][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-24 16:02:29.081][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-24 16:02:29.083][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-24 16:02:29.085][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-24 16:02:29.087][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-24 16:02:29.088][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-24 16:02:29.090][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-24 16:02:29.092][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-24 16:02:29.094][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-24 16:02:29.096][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-24 16:02:29.097][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-24 16:02:29.099][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-24 16:02:29.101][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-24 16:02:29.102][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-24 16:02:29.104][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-24 16:02:29.106][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-24 16:02:29.108][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-24 16:02:29.109][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-24 16:02:29.111][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-24 16:02:29.113][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-24 16:02:29.115][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-24 16:02:29.116][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-24 16:02:29.118][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-24 16:02:29.120][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-24 16:02:29.122][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-24 16:02:29.124][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-24 16:02:29.125][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-24 16:02:29.127][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-24 16:02:29.129][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-24 16:02:29.131][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-24 16:02:29.132][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-24 16:02:29.134][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-24 16:02:29.136][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-24 16:02:29.144][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-24 16:02:29.146][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:29.149][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:29.150][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.153][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:29.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:29.294][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:29.307][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:29.310][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.311][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-24 16:02:29.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:29.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.317][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.320][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-24 16:02:29.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:29.322][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.323][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-24 16:02:29.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:29.326][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-24 16:02:29.326][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-24 16:02:29.327][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:29.329][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:29.330][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:29.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:29.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.338][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:29.338][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-24 16:02:29.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:29.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:29.342][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.343][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:29.345][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-24 16:02:29.347][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.348][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-24 16:02:29.350][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:29.352][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.355][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.357][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:29.359][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:29.360][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.361][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-24 16:02:29.362][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-24 16:02:29.364][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-24 16:02:29.365][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:29.366][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:29.368][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:29.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:29.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.375][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.376][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:29.376][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:29.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:29.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:29.380][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.381][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:29.383][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-24 16:02:29.385][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:29.386][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-24 16:02:29.388][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.389][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:29.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.393][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.395][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:29.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:29.398][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.399][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-24 16:02:29.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.402][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:29.403][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:29.405][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:29.405][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:29.405][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:29.406][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:29.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:29.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.415][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:29.415][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:29.415][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:29.416][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:29.417][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:29.418][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.420][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:29.421][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-24 16:02:29.424][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.425][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-24 16:02:29.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.428][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:29.429][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.432][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.434][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:29.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:29.437][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.438][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-24 16:02:29.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:29.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-24 16:02:29.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:29.442][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:29.444][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:29.445][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:29.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.450][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:29.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:29.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:29.454][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:29.455][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:29.455][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:29.455][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:29.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:29.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:29.459][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:29.460][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:29.469][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-24 16:02:29.471][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:29.474][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:29.477][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-24 16:02:29.479][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:29.482][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-24 16:02:29.512][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:29.528][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2026-01-24 16:02:29.538][biodb::testThat]
biodb.INFO [2026-01-24 16:02:29.540][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-24 16:02:29.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:29.542][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:29.547][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2026-01-24 16:02:29.549][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:29.553][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-01-24 16:02:29.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:29.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:29.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:29.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:29.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:29.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:29.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.625][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:29.642][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.644][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.645][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.682][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:29.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.703][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:29.794][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2026-01-24 16:02:29.797][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:29.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:29.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:29.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:29.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:29.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:29.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:29.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:29.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.880][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.932][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:29.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.961][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.964][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.965][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:29.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.986][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:29.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:29.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:29.996][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:29.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.002][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.003][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.004][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.005][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.022][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.024][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.025][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.026][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.032][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.034][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.035][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.036][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.059][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2026-01-24 16:02:30.108][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:30.109][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2026-01-24 16:02:30.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:30.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:30.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:30.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:30.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:30.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:30.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:30.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.168][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.169][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.172][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.173][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.184][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:30.265][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2026-01-24 16:02:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.297][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:30.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:30.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:30.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:30.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:30.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:30.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:30.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:30.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.333][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.376][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.386][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:30.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.428][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.429][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.435][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.436][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.453][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.458][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.463][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.468][ef$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.469][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.471][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.472][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.473][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2026-01-24 16:02:30.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.489][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.490][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:30.492][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.493][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:30.500][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:30.501][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:30.502][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:30.504][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:30.514][biodb::testThat]
biodb.INFO [2026-01-24 16:02:30.515][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-24 16:02:30.516][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:30.518][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:30.520][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2026-01-24 16:02:30.524][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:30.528][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-24 16:02:30.529][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:30.531][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:30.532][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:30.533][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-24 16:02:30.717][biodb::testThat]
biodb.INFO [2026-01-24 16:02:30.718][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-24 16:02:30.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:30.720][biodb::testThat]
biodb.INFO [2026-01-24 16:02:30.729][biodb::testThat]
biodb.INFO [2026-01-24 16:02:30.730][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-24 16:02:30.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:30.733][biodb::testThat]
biodb.WARN [2026-01-24 16:02:30.754][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-24 16:02:30.779][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-24 16:02:30.790][biodb::testThat]
biodb.INFO [2026-01-24 16:02:30.791][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-24 16:02:30.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:30.793][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:30.816][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2026-01-24 16:02:30.887][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:30.928][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-24 16:02:30.941][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:30.943][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:30.944][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:30.945][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-24 16:02:31.043][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.045][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-24 16:02:31.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:31.047][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-24 16:02:31.108][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.109][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-24 16:02:31.111][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:31.112][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.122][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.123][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:31.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:31.126][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2026-01-24 16:02:31.186][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.188][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:31.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:31.190][biodb::testThat]
biodb.INFO [2026-01-24 16:02:31.203][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-24 16:02:31.205][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-01-24 16:02:31.206][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-24 16:02:31.207][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.209][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.211][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-24 16:02:31.226][biodb::testContext]
biodb.INFO [2026-01-24 16:02:31.227][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:31.228][biodb::testContext] Test context - Gene long tests
biodb.INFO [2026-01-24 16:02:31.230][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:31.231][biodb::testContext]
biodb.INFO [2026-01-24 16:02:31.233][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:31.235][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:31.240][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:31.241][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-24 16:02:31.242][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.247][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-24 16:02:31.249][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.253][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-24 16:02:31.255][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.259][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-24 16:02:31.261][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-24 16:02:31.262][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-24 16:02:31.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.267][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-24 16:02:31.268][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-24 16:02:31.269][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.274][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-24 16:02:31.276][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-24 16:02:31.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.280][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-24 16:02:31.282][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-24 16:02:31.283][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-24 16:02:31.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.288][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-24 16:02:31.289][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.294][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-24 16:02:31.295][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-24 16:02:31.296][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-24 16:02:31.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.301][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:31.302][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-24 16:02:31.303][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-24 16:02:31.305][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-24 16:02:31.306][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-24 16:02:31.307][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-24 16:02:31.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.312][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-24 16:02:31.313][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-24 16:02:31.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.318][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-24 16:02:31.319][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-24 16:02:31.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.324][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-24 16:02:31.325][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-24 16:02:31.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.330][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-24 16:02:31.331][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-24 16:02:31.332][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-24 16:02:31.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.337][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:31.338][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-24 16:02:31.349][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-24 16:02:31.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.354][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-24 16:02:31.355][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-24 16:02:31.357][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-24 16:02:31.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.362][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-24 16:02:31.364][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.365][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-24 16:02:31.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.373][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.375][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:31.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.379][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-24 16:02:31.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.381][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:31.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:31.384][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:31.384][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:31.384][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:31.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:31.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:31.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.394][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:31.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:31.398][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.400][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.401][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-24 16:02:31.404][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.405][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:31.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.408][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.413][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.415][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.416][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.417][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.418][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:31.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.422][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-24 16:02:31.424][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.425][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:31.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:31.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:31.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:31.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:31.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:31.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:31.433][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.436][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.437][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.438][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:31.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:31.441][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.442][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.444][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-24 16:02:31.446][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.447][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-24 16:02:31.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:31.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.459][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.460][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-24 16:02:31.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.463][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.465][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:31.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:31.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.475][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:31.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:31.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.480][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.481][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-24 16:02:31.484][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.485][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:31.486][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.489][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.490][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.491][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.494][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:31.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.497][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.498][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-24 16:02:31.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.501][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.503][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.505][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:31.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:31.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.512][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.513][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.514][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:31.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:31.517][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.518][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:31.521][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.619][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-24 16:02:31.621][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-24 16:02:31.623][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-24 16:02:31.625][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-24 16:02:31.626][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-24 16:02:31.628][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:31.630][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:31.632][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:31.634][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-24 16:02:31.635][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:31.637][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:31.639][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-24 16:02:31.641][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:31.643][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:31.644][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:31.646][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:31.648][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-24 16:02:31.650][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-24 16:02:31.651][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-24 16:02:31.653][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-24 16:02:31.655][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-24 16:02:31.657][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-24 16:02:31.658][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-24 16:02:31.660][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-24 16:02:31.662][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-24 16:02:31.664][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-24 16:02:31.665][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-24 16:02:31.667][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-24 16:02:31.669][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-24 16:02:31.671][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-24 16:02:31.672][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-24 16:02:31.674][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-24 16:02:31.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-24 16:02:31.678][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-24 16:02:31.680][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-24 16:02:31.682][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-24 16:02:31.684][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-24 16:02:31.688][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-24 16:02:31.689][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-24 16:02:31.691][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-24 16:02:31.693][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-24 16:02:31.695][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-24 16:02:31.697][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-24 16:02:31.698][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-24 16:02:31.700][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-24 16:02:31.702][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:31.704][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-24 16:02:31.705][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-24 16:02:31.707][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-24 16:02:31.709][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-24 16:02:31.711][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-24 16:02:31.713][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-24 16:02:31.714][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-24 16:02:31.716][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-24 16:02:31.718][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-24 16:02:31.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-24 16:02:31.721][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-24 16:02:31.723][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-24 16:02:31.725][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-24 16:02:31.727][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-24 16:02:31.728][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-24 16:02:31.730][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-24 16:02:31.732][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-24 16:02:31.734][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-24 16:02:31.735][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-24 16:02:31.737][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-24 16:02:31.739][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-24 16:02:31.741][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-24 16:02:31.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-24 16:02:31.745][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-24 16:02:31.746][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-24 16:02:31.748][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-24 16:02:31.750][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-24 16:02:31.752][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-24 16:02:31.754][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-24 16:02:31.755][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-24 16:02:31.757][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-24 16:02:31.759][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-24 16:02:31.761][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-24 16:02:31.763][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-24 16:02:31.764][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-24 16:02:31.766][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-24 16:02:31.768][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-24 16:02:31.770][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-24 16:02:31.772][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:31.773][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:31.774][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.777][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:31.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:31.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:31.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:31.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:31.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:31.931][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:31.933][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:31.935][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.937][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-24 16:02:31.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.939][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.940][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.942][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.943][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.944][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.945][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-24 16:02:31.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.948][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.949][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-24 16:02:31.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.952][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-24 16:02:31.952][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-24 16:02:31.953][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.955][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.956][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:31.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:31.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:31.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.964][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:31.964][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-24 16:02:31.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:31.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:31.968][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.969][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:31.971][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-24 16:02:31.973][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.975][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-24 16:02:31.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:31.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.982][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:31.985][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:31.986][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:31.987][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:31.989][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-24 16:02:31.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-24 16:02:31.992][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-24 16:02:31.993][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:31.994][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:31.996][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:31.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:31.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:32.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:32.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.007][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.007][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:32.008][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:32.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:32.011][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.012][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:32.014][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-24 16:02:32.016][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:32.018][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-24 16:02:32.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.020][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:32.022][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.028][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.030][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.035][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:32.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:32.038][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.039][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-24 16:02:32.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.042][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:32.043][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:32.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:32.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:32.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:32.046][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:32.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:32.048][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.050][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:32.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:32.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.056][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.056][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:32.056][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:32.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:32.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:32.059][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.061][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:32.063][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-24 16:02:32.067][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.069][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-24 16:02:32.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.072][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:32.073][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.076][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.077][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.079][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:32.080][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:32.081][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.083][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-24 16:02:32.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:32.085][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-24 16:02:32.085][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:32.087][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:32.088][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:32.089][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:32.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:32.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:32.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:32.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:32.098][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:32.100][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.100][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:32.100][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:32.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:32.104][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:32.106][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:32.107][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:32.109][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-24 16:02:32.111][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:32.113][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:32.115][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-24 16:02:32.117][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:32.119][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-24 16:02:32.128][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2026-01-24 16:02:32.170][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2026-01-24 16:02:32.175][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.177][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-24 16:02:32.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.179][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:32.186][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2026-01-24 16:02:32.187][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:32.191][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2026-01-24 16:02:32.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:32.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:32.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:32.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:32.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:32.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:32.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:32.220][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.221][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.224][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.231][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:32.232][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:32.234][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.235][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-24 16:02:32.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-24 16:02:32.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.242][ef$get] Asked field names are: location.
biodb.TRACE[2026-01-24 16:02:32.244][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-01-24 16:02:32.245][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.246][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.248][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2026-01-24 16:02:32.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2026-01-24 16:02:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.260][ef$get] Asked field names are: symbol.
biodb.TRACE[2026-01-24 16:02:32.261][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-01-24 16:02:32.262][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.263][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.265][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2026-01-24 16:02:32.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2026-01-24 16:02:32.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.271][ef$get] Asked field names are: synonyms.
biodb.TRACE[2026-01-24 16:02:32.272][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:32.274][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.275][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.277][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2026-01-24 16:02:32.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:32.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.282][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-01-24 16:02:32.284][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-01-24 16:02:32.285][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.286][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2026-01-24 16:02:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2026-01-24 16:02:32.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.305][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.310][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2026-01-24 16:02:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:32.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:32.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:32.357][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2026-01-24 16:02:32.361][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:32.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:32.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.368][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:32.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:32.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.375][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:32.392][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2026-01-24 16:02:32.433][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:32.458][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2026-01-24 16:02:32.459][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2026-01-24 16:02:32.463][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:32.465][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2026-01-24 16:02:32.467][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:32.468][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:32.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:32.470][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:32.533][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.535][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-24 16:02:32.536][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.537][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:32.540][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2026-01-24 16:02:32.542][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2026-01-24 16:02:32.543][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-24 16:02:32.545][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:32.547][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.548][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:32.549][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:32.550][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:32.611][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.613][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-24 16:02:32.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.615][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:32.619][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:32.621][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:32.622][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:32.623][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:32.629][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2026-01-24 16:02:32.641][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-24 16:02:32.642][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:32.644][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-24 16:02:32.646][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:32.647][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.648][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:32.649][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:32.674][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:32.754][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.755][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-24 16:02:32.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.757][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:32.768][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-24 16:02:32.769][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:32.771][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-24 16:02:32.773][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:32.774][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.776][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:32.777][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:32.778][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:32.842][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.844][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-24 16:02:32.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.846][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:32.851][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2026-01-24 16:02:32.852][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:32.854][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2026-01-24 16:02:32.856][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:32.857][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:32.858][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:32.859][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:32.861][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:32.921][biodb::testThat]
biodb.INFO [2026-01-24 16:02:32.922][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-24 16:02:32.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:32.925][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:33.016][biodb::testThat]
biodb.INFO [2026-01-24 16:02:33.018][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-24 16:02:33.021][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:33.023][biodb::testThat]
biodb.INFO [2026-01-24 16:02:33.043][biodb::testThat]
biodb.INFO [2026-01-24 16:02:33.045][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:33.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:33.050][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2026-01-24 16:02:33.143][biodb::testThat]
biodb.INFO [2026-01-24 16:02:33.144][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:33.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:33.146][biodb::testThat]
biodb.INFO [2026-01-24 16:02:33.155][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-24 16:02:33.156][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2026-01-24 16:02:33.157][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2026-01-24 16:02:33.159][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-24 16:02:33.160][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.162][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.165][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-24 16:02:33.171][biodb::testContext]
biodb.INFO [2026-01-24 16:02:33.173][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:33.174][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2026-01-24 16:02:33.175][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:33.176][biodb::testContext]
biodb.INFO [2026-01-24 16:02:33.179][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:33.181][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:33.185][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:33.186][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-24 16:02:33.188][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.192][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-24 16:02:33.194][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.198][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-24 16:02:33.199][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.204][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-24 16:02:33.205][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-24 16:02:33.207][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-24 16:02:33.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.211][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-24 16:02:33.212][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-24 16:02:33.214][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.218][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-24 16:02:33.220][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-24 16:02:33.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.224][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-24 16:02:33.230][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-24 16:02:33.231][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-24 16:02:33.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.236][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-24 16:02:33.237][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.242][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-24 16:02:33.243][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-24 16:02:33.244][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-24 16:02:33.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.249][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:33.250][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-24 16:02:33.251][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-24 16:02:33.253][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-24 16:02:33.254][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-24 16:02:33.255][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-24 16:02:33.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.260][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-24 16:02:33.261][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-24 16:02:33.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.266][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-24 16:02:33.267][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-24 16:02:33.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.271][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-24 16:02:33.273][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-24 16:02:33.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.277][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-24 16:02:33.278][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-24 16:02:33.280][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-24 16:02:33.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.284][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:33.285][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-24 16:02:33.296][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-24 16:02:33.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.300][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-24 16:02:33.302][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-24 16:02:33.303][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-24 16:02:33.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.308][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-24 16:02:33.310][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.311][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-24 16:02:33.313][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.314][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:33.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.318][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.320][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:33.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:33.323][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.324][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-24 16:02:33.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:33.326][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.328][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:33.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:33.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:33.329][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:33.329][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:33.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:33.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.334][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:33.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.338][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:33.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:33.342][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.343][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.345][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-24 16:02:33.347][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.348][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:33.350][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:33.352][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.355][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.357][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:33.359][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:33.360][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.361][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-24 16:02:33.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:33.364][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.365][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.366][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:33.366][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:33.366][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:33.366][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:33.366][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:33.368][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:33.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:33.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.375][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.376][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:33.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:33.380][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.381][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.382][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-24 16:02:33.385][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.386][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-24 16:02:33.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:33.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.392][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.394][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:33.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:33.397][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.398][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-24 16:02:33.399][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:33.401][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.403][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:33.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:33.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.413][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:33.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:33.421][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.422][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.423][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-24 16:02:33.426][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.427][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:33.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:33.431][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.433][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.435][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:33.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:33.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.439][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-24 16:02:33.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:33.442][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.443][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:33.444][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:33.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:33.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:33.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:33.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:33.454][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.455][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:33.456][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:33.457][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:33.459][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:33.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:33.461][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.552][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-24 16:02:33.554][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-24 16:02:33.556][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-24 16:02:33.558][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-24 16:02:33.559][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-24 16:02:33.561][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:33.563][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:33.564][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:33.566][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-24 16:02:33.568][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:33.569][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:33.571][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-24 16:02:33.573][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:33.575][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:33.576][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:33.578][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:33.580][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-24 16:02:33.581][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-24 16:02:33.583][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-24 16:02:33.585][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-24 16:02:33.586][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-24 16:02:33.588][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-24 16:02:33.595][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-24 16:02:33.596][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-24 16:02:33.599][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-24 16:02:33.600][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-24 16:02:33.602][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-24 16:02:33.604][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-24 16:02:33.606][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-24 16:02:33.607][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-24 16:02:33.609][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-24 16:02:33.611][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-24 16:02:33.613][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-24 16:02:33.614][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-24 16:02:33.616][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-24 16:02:33.618][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-24 16:02:33.620][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-24 16:02:33.621][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-24 16:02:33.623][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-24 16:02:33.625][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-24 16:02:33.627][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-24 16:02:33.628][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-24 16:02:33.630][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-24 16:02:33.632][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-24 16:02:33.634][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-24 16:02:33.635][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:33.637][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-24 16:02:33.639][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-24 16:02:33.641][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-24 16:02:33.642][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-24 16:02:33.644][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-24 16:02:33.646][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-24 16:02:33.647][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-24 16:02:33.649][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-24 16:02:33.651][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-24 16:02:33.653][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-24 16:02:33.654][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-24 16:02:33.656][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-24 16:02:33.658][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-24 16:02:33.660][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-24 16:02:33.661][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-24 16:02:33.663][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-24 16:02:33.665][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-24 16:02:33.667][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-24 16:02:33.668][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-24 16:02:33.670][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-24 16:02:33.672][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-24 16:02:33.673][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-24 16:02:33.675][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-24 16:02:33.677][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-24 16:02:33.679][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-24 16:02:33.680][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-24 16:02:33.682][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-24 16:02:33.684][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-24 16:02:33.686][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-24 16:02:33.687][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-24 16:02:33.689][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-24 16:02:33.691][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-24 16:02:33.693][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-24 16:02:33.694][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-24 16:02:33.696][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-24 16:02:33.698][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-24 16:02:33.700][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-24 16:02:33.702][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-24 16:02:33.704][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:33.706][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:33.708][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.711][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:33.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:33.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:33.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:33.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:33.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:33.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:33.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:34.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:34.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:34.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:34.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:34.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:34.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:34.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:34.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:34.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:34.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:34.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:34.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:34.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:34.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:34.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:34.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:34.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:34.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:34.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:34.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:34.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:34.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:34.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:34.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:34.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:34.053][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:34.057][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:34.061][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.064][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-24 16:02:34.066][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.069][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:34.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.074][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.076][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.078][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.081][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-24 16:02:34.083][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:34.086][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.088][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-24 16:02:34.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:34.093][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-24 16:02:34.093][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-24 16:02:34.096][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:34.098][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:34.100][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:34.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:34.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.112][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.113][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:34.113][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-24 16:02:34.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:34.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:34.117][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.119][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:34.121][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-24 16:02:34.123][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.125][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-24 16:02:34.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:34.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.132][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.134][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.136][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:34.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:34.141][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.142][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-24 16:02:34.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-24 16:02:34.145][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-24 16:02:34.147][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:34.148][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:34.149][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:34.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.153][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:34.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.156][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.158][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:34.158][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:34.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:34.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:34.161][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.162][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:34.164][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-24 16:02:34.166][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:34.168][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-24 16:02:34.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:34.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.173][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.174][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.175][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.176][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:34.178][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:34.179][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.180][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-24 16:02:34.181][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.183][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:34.184][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:34.186][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:34.186][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:34.186][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:34.187][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:34.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.195][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:34.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.199][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:34.199][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:34.199][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:34.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:34.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:34.203][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.204][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:34.206][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-24 16:02:34.208][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.210][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-24 16:02:34.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:34.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.216][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.218][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:34.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:34.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.222][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-24 16:02:34.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:34.224][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-24 16:02:34.224][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:34.226][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:34.227][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:34.228][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:34.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:34.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:34.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:34.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:34.236][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:34.236][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:34.236][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:34.238][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:34.239][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:34.240][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:34.241][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:34.243][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-24 16:02:34.245][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:34.247][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:34.249][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-24 16:02:34.250][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:34.252][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-24 16:02:34.261][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-24 16:02:34.266][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2026-01-24 16:02:34.271][biodb::testThat]
biodb.INFO [2026-01-24 16:02:34.272][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-24 16:02:34.274][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:34.275][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:34.278][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2026-01-24 16:02:34.280][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:34.283][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-01-24 16:02:34.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:34.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:34.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:34.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:34.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:34.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:34.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:34.303][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.305][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.306][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.307][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.314][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.315][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.316][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.317][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.324][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.325][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.327][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.328][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.335][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.336][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.337][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.338][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.345][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.347][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.348][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.349][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.351][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.356][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.357][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.359][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.360][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.367][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:34.368][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.369][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.370][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.372][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:34.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.384][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.385][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.386][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.387][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:34.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:34.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.398][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:34.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:34.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:34.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:34.407][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.409][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:34.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:34.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.416][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.417][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.418][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.419][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.426][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:34.428][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.429][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.430][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:34.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.437][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.439][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.440][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.441][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.448][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.450][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.451][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.452][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.459][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-01-24 16:02:34.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.474][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-01-24 16:02:34.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.484][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:34.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.489][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-01-24 16:02:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:34.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.504][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-01-24 16:02:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:34.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.520][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-01-24 16:02:34.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:34.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:34.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.540][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.577][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:34.612][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2026-01-24 16:02:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:34.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:34.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.620][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:34.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.625][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:34.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:34.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:34.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:34.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:34.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:34.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:34.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:34.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:34.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.714][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.753][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.755][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.757][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.779][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:34.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.795][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:34.796][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.797][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.798][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.800][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.831][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:34.833][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.834][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.835][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:34.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.868][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.871][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.872][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:34.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.889][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.905][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.906][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.907][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.909][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:34.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:34.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.937][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.942][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.943][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.949][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.951][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:34.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.985][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.986][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.988][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.989][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.021][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.023][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.024][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.025][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.058][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.059][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.061][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.062][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.090][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.095][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.096][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.097][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.099][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.136][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.138][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.139][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.141][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.158][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.174][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.175][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.177][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.178][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.210][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.212][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.213][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.214][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.247][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.249][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.251][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.284][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.285][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.286][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.287][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.305][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.308][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.309][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.316][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.317][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.323][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.325][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.332][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.333][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.334][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.335][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.342][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.344][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.345][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.346][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.353][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.354][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.356][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.357][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.364][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.365][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.367][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.368][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.376][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:35.377][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:35.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.380][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.388][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.390][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.391][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.397][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.400][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.401][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.408][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:35.409][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:35.410][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.412][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.418][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.421][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.422][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.429][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.430][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.432][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.433][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.439][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.442][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.443][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.450][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.452][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.453][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.454][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.461][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.462][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.463][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.465][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.472][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2026-01-24 16:02:35.474][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:35.475][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2026-01-24 16:02:35.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:35.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:35.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:35.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:35.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:35.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:35.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:35.493][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.495][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.496][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.497][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.504][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.505][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.507][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.508][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.515][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.516][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.517][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.518][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.531][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.532][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.533][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.534][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.541][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.543][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.544][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.545][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.552][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.553][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.554][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.555][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.562][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:35.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.565][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.566][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2026-01-24 16:02:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.573][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:35.574][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:35.575][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.577][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:35.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:35.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.586][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.587][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:35.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:35.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.594][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.595][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.596][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.598][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:35.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.604][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:35.606][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:35.607][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.608][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.610][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:35.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:35.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.615][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:35.617][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.618][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.619][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2026-01-24 16:02:35.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.627][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.629][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.631][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.633][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:35.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.639][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.640][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.642][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.643][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:35.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.651][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2026-01-24 16:02:35.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.657][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:35.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.668][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2026-01-24 16:02:35.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.673][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.678][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:35.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.684][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2026-01-24 16:02:35.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:35.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.699][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2026-01-24 16:02:35.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.720][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2026-01-24 16:02:35.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:35.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:35.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:35.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.741][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:35.791][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2026-01-24 16:02:35.793][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:35.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:35.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.798][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:35.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:35.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:35.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:35.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:35.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:35.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:35.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:35.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:35.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:35.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.823][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.840][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.897][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:35.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.926][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.928][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.929][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:35.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:35.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.962][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.965][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.966][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:35.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:35.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:35.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:35.999][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.001][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.002][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.020][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.031][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.036][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.037][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.038][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.040][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.057][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.062][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.078][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.079][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.081][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.082][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.083][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.104][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.115][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.116][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.117][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.118][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.120][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.146][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.151][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.153][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.154][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.155][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.156][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.188][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.190][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.191][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.192][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.228][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.229][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.246][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.267][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.268][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.270][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.271][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.293][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.303][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.305][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.306][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.307][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.340][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.342][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.343][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.344][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.377][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.378][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.381][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.414][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.415][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.416][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.417][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.456][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.459][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.460][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.477][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:36.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:36.480][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.481][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.488][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.489][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2026-01-24 16:02:36.491][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.492][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.499][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.500][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2026-01-24 16:02:36.502][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.503][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.510][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.512][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2026-01-24 16:02:36.513][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.515][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.522][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.523][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-24 16:02:36.525][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.526][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.533][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.535][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-24 16:02:36.537][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.538][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.545][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-24 16:02:36.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-24 16:02:36.548][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.549][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.556][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-24 16:02:36.558][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-24 16:02:36.559][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.560][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-24 16:02:36.570][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.571][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.577][ef$get] Asked field names are: logp.
biodb.TRACE[2026-01-24 16:02:36.579][ef$get] Realnames of fields are: logp.
biodb.TRACE[2026-01-24 16:02:36.580][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.581][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.588][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.590][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:36.591][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.592][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.599][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:36.601][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-24 16:02:36.602][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.603][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.610][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.611][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.612][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.614][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.620][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.622][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2026-01-24 16:02:36.623][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.624][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:36.631][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.632][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2026-01-24 16:02:36.633][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.634][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:36.650][biodb::testThat]
biodb.INFO [2026-01-24 16:02:36.651][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-24 16:02:36.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:36.654][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:36.656][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:36.660][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:36.662][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:36.663][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:36.665][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:36.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:36.667][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:36.668][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:36.726][biodb::testThat]
biodb.INFO [2026-01-24 16:02:36.727][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-24 16:02:36.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:36.730][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:36.734][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:36.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:36.737][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:36.738][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:36.739][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2026-01-24 16:02:36.751][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-24 16:02:36.822][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:36.824][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:36.825][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:36.827][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:36.828][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:36.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:36.853][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:36.913][biodb::testThat]
biodb.INFO [2026-01-24 16:02:36.914][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-24 16:02:36.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:36.917][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:36.927][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-24 16:02:36.928][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:36.930][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:36.932][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:36.933][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:36.934][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:36.935][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:36.937][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.001][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.002][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-24 16:02:37.004][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.005][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.010][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-24 16:02:37.011][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:37.013][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.014][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.016][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.017][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.018][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.020][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.078][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.079][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-24 16:02:37.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.081][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.145][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.146][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-24 16:02:37.147][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.148][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.206][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.208][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:37.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.210][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.268][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.269][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:37.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.271][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-01-24 16:02:37.345][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:37.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:37.348][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:37.349][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:37.350][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:37.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:37.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:37.354][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:37.357][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.358][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2026-01-24 16:02:37.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.360][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.370][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2026-01-24 16:02:37.371][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:37.373][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.374][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.376][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.377][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.378][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.379][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.443][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.444][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2026-01-24 16:02:37.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.447][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.450][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:37.452][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:37.453][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.455][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.456][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.457][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.459][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.460][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.518][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.519][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2026-01-24 16:02:37.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.522][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.525][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:37.527][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:37.529][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.530][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.531][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.533][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.534][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.535][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.594][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.600][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2026-01-24 16:02:37.601][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.603][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.607][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:37.608][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:37.610][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.611][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.613][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.614][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.616][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.617][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2026-01-24 16:02:37.676][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-24 16:02:37.677][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-24 16:02:37.678][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:37.680][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:37.681][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:37.682][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-24 16:02:37.684][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:37.685][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:37.687][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.688][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2026-01-24 16:02:37.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.691][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.695][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:37.696][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:37.698][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.700][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.701][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.702][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.704][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.705][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.770][biodb::testThat]
biodb.INFO [2026-01-24 16:02:37.771][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2026-01-24 16:02:37.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:37.774][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:37.777][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2026-01-24 16:02:37.779][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2026-01-24 16:02:37.781][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:37.782][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:37.784][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:37.785][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:37.786][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:37.787][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2026-01-24 16:02:37.848][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-24 16:02:37.850][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2026-01-24 16:02:37.851][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-24 16:02:37.852][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:37.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:37.854][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:37.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:37.856][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-24 16:02:37.863][biodb::testContext]
biodb.INFO [2026-01-24 16:02:37.864][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:37.865][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2026-01-24 16:02:37.866][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-24 16:02:37.868][biodb::testContext]
biodb.INFO [2026-01-24 16:02:37.870][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:37.872][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:37.877][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:37.878][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-24 16:02:37.880][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.885][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-24 16:02:37.886][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.891][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-24 16:02:37.892][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.897][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-24 16:02:37.898][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-24 16:02:37.899][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-24 16:02:37.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.904][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-24 16:02:37.905][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-24 16:02:37.907][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.911][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-24 16:02:37.913][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-24 16:02:37.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.918][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-24 16:02:37.919][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-24 16:02:37.920][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-24 16:02:37.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.925][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-24 16:02:37.926][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.936][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-24 16:02:37.938][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-24 16:02:37.939][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-24 16:02:37.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.944][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:37.945][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-24 16:02:37.946][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-24 16:02:37.947][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-24 16:02:37.949][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-24 16:02:37.950][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-24 16:02:37.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.955][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-24 16:02:37.956][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-24 16:02:37.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.961][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-24 16:02:37.962][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-24 16:02:37.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.966][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-24 16:02:37.968][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-24 16:02:37.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.972][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-24 16:02:37.974][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-24 16:02:37.975][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-24 16:02:37.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.980][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-24 16:02:37.981][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-24 16:02:37.991][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-24 16:02:37.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:37.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:37.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:37.997][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-24 16:02:37.998][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-24 16:02:37.999][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-24 16:02:38.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.004][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-24 16:02:38.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.008][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-24 16:02:38.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.017][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:38.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.019][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.021][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-24 16:02:38.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.023][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.026][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:38.026][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:38.026][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:38.026][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:38.026][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:38.027][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:38.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.036][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.038][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.039][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.040][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.042][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-24 16:02:38.044][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.046][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:38.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.048][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.055][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:38.056][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.057][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.059][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-24 16:02:38.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.061][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.063][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.064][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:38.064][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:38.064][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:38.064][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-24 16:02:38.064][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-24 16:02:38.065][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:38.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.069][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.073][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.074][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.078][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.079][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.081][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-24 16:02:38.083][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.084][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-24 16:02:38.086][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.087][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.091][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.092][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.093][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-24 16:02:38.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.096][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.097][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-24 16:02:38.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.100][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.103][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.104][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:38.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.106][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.118][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.122][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.123][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.124][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-24 16:02:38.127][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.128][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-24 16:02:38.129][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.136][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.137][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-24 16:02:38.138][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.139][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.141][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-24 16:02:38.142][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.143][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.146][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.147][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-24 16:02:38.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.156][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.158][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.159][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.161][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:38.163][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.258][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-24 16:02:38.260][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-24 16:02:38.262][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-24 16:02:38.263][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-24 16:02:38.265][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-24 16:02:38.267][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-24 16:02:38.269][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:38.270][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:38.272][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-24 16:02:38.274][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-24 16:02:38.275][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-24 16:02:38.277][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-24 16:02:38.287][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-24 16:02:38.289][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-24 16:02:38.291][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:38.293][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:38.295][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-24 16:02:38.297][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-24 16:02:38.298][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-24 16:02:38.300][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-24 16:02:38.302][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-24 16:02:38.304][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-24 16:02:38.305][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-24 16:02:38.307][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-24 16:02:38.309][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-24 16:02:38.311][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-24 16:02:38.312][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-24 16:02:38.314][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-24 16:02:38.316][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-24 16:02:38.318][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-24 16:02:38.319][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-24 16:02:38.321][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-24 16:02:38.323][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-24 16:02:38.325][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-24 16:02:38.327][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-24 16:02:38.328][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-24 16:02:38.330][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-24 16:02:38.332][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-24 16:02:38.333][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-24 16:02:38.335][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-24 16:02:38.337][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-24 16:02:38.339][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-24 16:02:38.341][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-24 16:02:38.342][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-24 16:02:38.344][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-24 16:02:38.346][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:38.348][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-24 16:02:38.349][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-24 16:02:38.351][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-24 16:02:38.353][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-24 16:02:38.355][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-24 16:02:38.357][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-24 16:02:38.359][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-24 16:02:38.360][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-24 16:02:38.362][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-24 16:02:38.364][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-24 16:02:38.366][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-24 16:02:38.367][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-24 16:02:38.369][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-24 16:02:38.371][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-24 16:02:38.373][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-24 16:02:38.374][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-24 16:02:38.376][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-24 16:02:38.378][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-24 16:02:38.380][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-24 16:02:38.382][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-24 16:02:38.383][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-24 16:02:38.385][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-24 16:02:38.387][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-24 16:02:38.389][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-24 16:02:38.390][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-24 16:02:38.392][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-24 16:02:38.394][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-24 16:02:38.396][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-24 16:02:38.398][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-24 16:02:38.399][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-24 16:02:38.401][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-24 16:02:38.403][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-24 16:02:38.405][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-24 16:02:38.407][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-24 16:02:38.408][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-24 16:02:38.410][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-24 16:02:38.412][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-24 16:02:38.414][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-24 16:02:38.416][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-24 16:02:38.417][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-24 16:02:38.418][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.421][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-24 16:02:38.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-24 16:02:38.559][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2026-01-24 16:02:38.561][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2026-01-24 16:02:38.563][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.565][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2026-01-24 16:02:38.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.567][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.569][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.570][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.571][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.572][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.574][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2026-01-24 16:02:38.575][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.576][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.578][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2026-01-24 16:02:38.579][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.581][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2026-01-24 16:02:38.581][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2026-01-24 16:02:38.582][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.584][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.585][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:38.587][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.588][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.590][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.594][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.595][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2026-01-24 16:02:38.595][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2026-01-24 16:02:38.596][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.598][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.599][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.600][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.602][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2026-01-24 16:02:38.604][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.606][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2026-01-24 16:02:38.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.613][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.614][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.615][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:38.617][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.618][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.619][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2026-01-24 16:02:38.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2026-01-24 16:02:38.622][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2026-01-24 16:02:38.624][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.625][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:38.627][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-24 16:02:38.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.636][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.640][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.641][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:38.641][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:38.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.646][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.647][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.648][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2026-01-24 16:02:38.651][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.652][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2026-01-24 16:02:38.653][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.655][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.656][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.657][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.658][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.661][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:38.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.665][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2026-01-24 16:02:38.666][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.667][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2026-01-24 16:02:38.669][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.670][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-24 16:02:38.670][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-24 16:02:38.670][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-24 16:02:38.672][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:38.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.679][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.680][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:38.680][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:38.680][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:38.681][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.682][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.684][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.685][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:38.687][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-24 16:02:38.689][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.690][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2026-01-24 16:02:38.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-24 16:02:38.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.697][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.698][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.699][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-24 16:02:38.700][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-24 16:02:38.702][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.703][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2026-01-24 16:02:38.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-24 16:02:38.706][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2026-01-24 16:02:38.706][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2026-01-24 16:02:38.707][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-24 16:02:38.708][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-24 16:02:38.709][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2026-01-24 16:02:38.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.713][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-24 16:02:38.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-24 16:02:38.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-24 16:02:38.717][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-24 16:02:38.718][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:38.718][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2026-01-24 16:02:38.718][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2026-01-24 16:02:38.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-24 16:02:38.720][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-24 16:02:38.721][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-24 16:02:38.723][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2026-01-24 16:02:38.724][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2026-01-24 16:02:38.726][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-24 16:02:38.728][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-24 16:02:38.730][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2026-01-24 16:02:38.732][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-24 16:02:38.734][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2026-01-24 16:02:38.740][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2026-01-24 16:02:38.746][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2026-01-24 16:02:38.751][biodb::testThat]
biodb.INFO [2026-01-24 16:02:38.752][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-24 16:02:38.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:38.755][biodb::testThat]
biodb.TRACE[2026-01-24 16:02:38.758][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2026-01-24 16:02:38.760][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2026-01-24 16:02:38.764][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2026-01-24 16:02:38.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-24 16:02:38.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:38.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:38.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:38.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:38.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:38.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-24 16:02:38.781][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.783][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.784][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.785][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.792][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:38.793][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:38.794][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.796][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.797][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:38.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:38.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.813][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.824][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-24 16:02:38.860][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2026-01-24 16:02:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.868][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2026-01-24 16:02:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2026-01-24 16:02:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.873][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:38.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2026-01-24 16:02:38.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:38.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-24 16:02:38.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-24 16:02:38.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:38.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-24 16:02:38.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:38.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-24 16:02:38.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.954][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.959][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.964][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2026-01-24 16:02:38.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:38.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:38.997][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:38.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:39.000][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.001][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:39.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.017][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.023][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.028][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.033][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.034][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.035][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.036][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.053][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-24 16:02:39.054][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-24 16:02:39.056][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.057][ef$get] fields variable is a list.
biodb.TRACE[2026-01-24 16:02:39.063][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.065][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-24 16:02:39.066][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-24 16:02:39.067][ef$get] fields variable is a list.
biodb.INFO [2026-01-24 16:02:39.077][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.078][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-24 16:02:39.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.081][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:39.083][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-01-24 16:02:39.087][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:39.089][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:39.090][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:39.091][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:39.093][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:39.094][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:39.095][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.158][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.159][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-24 16:02:39.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.162][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.170][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.171][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-24 16:02:39.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.173][biodb::testThat]
biodb.WARN [2026-01-24 16:02:39.176][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-24 16:02:39.180][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-24 16:02:39.191][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.192][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-24 16:02:39.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.195][biodb::testThat]
biodb.DEBUG[2026-01-24 16:02:39.200][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2026-01-24 16:02:39.264][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2026-01-24 16:02:39.266][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2026-01-24 16:02:39.268][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2026-01-24 16:02:39.269][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2026-01-24 16:02:39.270][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2026-01-24 16:02:39.271][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2026-01-24 16:02:39.296][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.360][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.361][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-24 16:02:39.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.363][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.423][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.424][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-24 16:02:39.425][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.427][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.490][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.491][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:39.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.494][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.552][biodb::testThat]
biodb.INFO [2026-01-24 16:02:39.553][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-24 16:02:39.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-24 16:02:39.556][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2026-01-24 16:02:39.620][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-24 16:02:39.622][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2026-01-24 16:02:39.623][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-24 16:02:39.624][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-24 16:02:39.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-24 16:02:39.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-24 16:02:39.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-24 16:02:39.628][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-24 16:02:39.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)