Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-11 23:55 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
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 7/30HostnameOS / ArchCHECK
biodbNcbi 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-11 09:55 -0400 (Sat, 11 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: devel
git_last_commit: ad86d6a
git_last_commit_date: 2025-07-24 10:47:22 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on lconway

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: 1.13.1
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_1.13.1.tar.gz
StartedAt: 2025-10-11 16:01:11 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 16:02:06 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 55.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 [2025-10-11 16:01:58.862][biodb::testContext]
biodb.INFO [2025-10-11 16:01:58.865][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:01:58.866][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-10-11 16:01:58.866][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:01:58.867][biodb::testContext]
biodb.INFO [2025-10-11 16:01:58.872][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:01:58.874][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:01:58.879][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:01:58.880][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:01:58.881][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.884][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:01:58.898][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.900][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[2025-10-11 16:01:58.901][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:01:58.902][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.913][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:01:58.914][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:01:58.915][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:01:58.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.917][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[2025-10-11 16:01:58.918][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:01:58.919][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:01:58.919][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.922][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:01:58.923][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:01:58.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.925][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[2025-10-11 16:01:58.926][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:01:58.927][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:01:58.927][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:01:58.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.930][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:01:58.931][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.933][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[2025-10-11 16:01:58.934][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:01:58.935][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:01:58.936][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:01:58.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.939][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:01:58.940][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:01:58.940][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:01:58.941][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:01:58.942][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:01:58.943][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:01:58.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.945][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[2025-10-11 16:01:58.946][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:01:58.946][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:01:58.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.949][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:01:58.950][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:01:58.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.952][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[2025-10-11 16:01:58.952][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:01:58.953][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:01:58.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.956][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:01:58.957][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:01:58.958][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:01:58.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.960][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[2025-10-11 16:01:58.961][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:01:58.961][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:01:58.979][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:01:58.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:01:58.982][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:01:58.983][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:01:58.984][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:01:58.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:58.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:58.986][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[2025-10-11 16:01:58.988][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:01:59.012][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.023][self$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[2025-10-11 16:01:59.024][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.027][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.028][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.029][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:01:59.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.030][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.031][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:01:59.032][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.032][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.033][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.034][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:01:59.034][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:01:59.034][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:01:59.034][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:01:59.034][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:01:59.035][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:01:59.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.039][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.041][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.042][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.043][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:01:59.044][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.045][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:01:59.046][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.046][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.047][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.053][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:01:59.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.057][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:01:59.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.058][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.060][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:01:59.060][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:01:59.060][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:01:59.060][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:01:59.060][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:01:59.061][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:01:59.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.066][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.067][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.069][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.070][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:01:59.071][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.072][self$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[2025-10-11 16:01:59.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.076][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.077][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:01:59.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.079][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.079][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:01:59.080][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.081][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.082][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.082][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:01:59.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.087][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.088][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.089][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.089][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.090][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.091][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.092][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:01:59.093][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.094][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:01:59.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.095][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.097][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.098][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.099][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:01:59.100][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.101][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.101][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:01:59.102][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.103][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.105][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.105][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:01:59.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.111][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.113][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.114][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:01:59.117][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.118][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[2025-10-11 16:01:59.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.122][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[2025-10-11 16:01:59.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.125][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[2025-10-11 16:01:59.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.129][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[2025-10-11 16:01:59.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.132][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[2025-10-11 16:01:59.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.136][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[2025-10-11 16:01:59.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.140][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[2025-10-11 16:01:59.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.143][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[2025-10-11 16:01:59.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.147][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[2025-10-11 16:01:59.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.150][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[2025-10-11 16:01:59.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.154][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[2025-10-11 16:01:59.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.157][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[2025-10-11 16:01:59.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.161][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[2025-10-11 16:01:59.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.165][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[2025-10-11 16:01:59.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.168][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[2025-10-11 16:01:59.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.172][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[2025-10-11 16:01:59.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.175][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[2025-10-11 16:01:59.176][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:01:59.179][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:01:59.181][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:01:59.186][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:01:59.187][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:01:59.188][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:01:59.189][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:01:59.190][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:01:59.191][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:01:59.192][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:01:59.193][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:01:59.194][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:01:59.195][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:01:59.196][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:01:59.198][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:01:59.199][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:01:59.200][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:01:59.201][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:01:59.202][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:01:59.203][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:01:59.204][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:01:59.205][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:01:59.206][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:01:59.207][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:01:59.208][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:01:59.209][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:01:59.210][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:01:59.211][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:01:59.212][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:01:59.214][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:01:59.215][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:01:59.216][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:01:59.217][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:01:59.218][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:01:59.219][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:01:59.220][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:01:59.221][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:01:59.222][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:01:59.224][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:01:59.225][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:01:59.226][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:01:59.227][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:01:59.228][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:01:59.229][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:01:59.230][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:01:59.231][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:01:59.232][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:01:59.233][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:01:59.234][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:01:59.235][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:01:59.237][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:01:59.238][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:01:59.239][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:01:59.240][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:01:59.241][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:01:59.242][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:01:59.243][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:01:59.244][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:01:59.245][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:01:59.246][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:01:59.247][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:01:59.248][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:01:59.249][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:01:59.250][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:01:59.251][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:01:59.252][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:01:59.253][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:01:59.254][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:01:59.255][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:01:59.256][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:01:59.257][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:01:59.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:01:59.259][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:01:59.260][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:01:59.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:01:59.263][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:01:59.264][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:01:59.265][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:01:59.266][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:01:59.267][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:01:59.268][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:01:59.269][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:01:59.270][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:01:59.275][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:01:59.276][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:01:59.278][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:01:59.279][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.281][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.281][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[2025-10-11 16:01:59.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.288][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[2025-10-11 16:01:59.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.294][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[2025-10-11 16:01:59.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.299][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[2025-10-11 16:01:59.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.304][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[2025-10-11 16:01:59.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.314][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[2025-10-11 16:01:59.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.318][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[2025-10-11 16:01:59.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.323][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[2025-10-11 16:01:59.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.329][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[2025-10-11 16:01:59.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.334][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[2025-10-11 16:01:59.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.339][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[2025-10-11 16:01:59.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.344][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[2025-10-11 16:01:59.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.349][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[2025-10-11 16:01:59.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.354][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[2025-10-11 16:01:59.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.359][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[2025-10-11 16:01:59.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.364][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[2025-10-11 16:01:59.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:01:59.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.369][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[2025-10-11 16:01:59.371][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-11 16:01:59.378][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:01:59.380][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.381][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-11 16:01:59.381][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.382][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.383][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.384][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.384][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.385][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.386][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-11 16:01:59.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.388][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-11 16:01:59.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.390][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-11 16:01:59.390][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-11 16:01:59.391][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.392][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.392][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:01:59.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.397][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:01:59.397][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-11 16:01:59.398][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.399][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.400][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.401][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.402][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-11 16:01:59.403][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.404][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-11 16:01:59.405][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.405][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.406][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.408][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.409][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:01:59.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.411][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.412][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-11 16:01:59.412][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-11 16:01:59.413][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-11 16:01:59.414][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.415][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:01:59.416][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:01:59.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.418][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.421][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:01:59.421][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:01:59.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.423][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.424][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.425][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-11 16:01:59.427][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.427][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-11 16:01:59.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.430][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.432][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.433][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:01:59.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.435][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.440][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.441][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:01:59.442][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.443][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:01:59.443][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:01:59.443][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:01:59.444][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:01:59.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.449][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:01:59.449][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:01:59.449][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:01:59.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.451][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.452][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:01:59.453][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-11 16:01:59.455][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.455][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-11 16:01:59.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:01:59.458][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.459][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.460][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.461][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:01:59.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:01:59.462][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.463][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-11 16:01:59.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:01:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-11 16:01:59.465][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:01:59.466][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:01:59.467][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:01:59.467][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:01:59.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:01:59.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:01:59.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:01:59.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:01:59.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:01:59.473][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:01:59.473][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:01:59.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:01:59.474][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:01:59.475][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:01:59.476][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:01:59.480][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-11 16:01:59.482][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:01:59.483][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:01:59.484][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-11 16:01:59.485][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:01:59.486][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-11 16:01:59.503][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:01:59.514][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-10-11 16:01:59.521][biodb::testThat]
biodb.INFO [2025-10-11 16:01:59.522][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:01:59.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:01:59.523][biodb::testThat]
biodb.TRACE[2025-10-11 16:01:59.527][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-10-11 16:01:59.528][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:01:59.531][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-11 16:01:59.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:01:59.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:01:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.578][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.597][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.598][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.623][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.626][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:01:59.678][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-10-11 16:01:59.721][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:01:59.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:01:59.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:01:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:01:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:01:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:01:59.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:01:59.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:01:59.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.775][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.804][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.807][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.810][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.832][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.833][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.835][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.847][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.854][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.857][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.858][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.859][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.860][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.870][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.871][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.872][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.877][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.879][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.895][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-10-11 16:01:59.928][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:01:59.929][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-11 16:01:59.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:01:59.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:01:59.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:01:59.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:01:59.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:01:59.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:01:59.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:01:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.966][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.967][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.968][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:01:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:01:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.973][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.983][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:01:59.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:01:59.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:01:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:01:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:01:59.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:00.006][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-10-11 16:02:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.030][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:00.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:00.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.037][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:00.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:00.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:00.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.086][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.116][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.119][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:02:00.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.137][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.143][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:02:00.144][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.146][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.147][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-11 16:02:00.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.158][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.159][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.161][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:00.165][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:00.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:00.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:00.168][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:00.176][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.176][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:00.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.178][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:00.180][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-10-11 16:02:00.183][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:00.185][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-11 16:02:00.187][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:00.188][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:00.188][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:00.189][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:00.222][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.223][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:00.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.225][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.231][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.232][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:00.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.233][biodb::testThat]
biodb.WARN [2025-10-11 16:02:00.256][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-11 16:02:00.273][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-11 16:02:00.282][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.283][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:00.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.284][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:00.299][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-10-11 16:02:00.343][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:00.366][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-11 16:02:00.368][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:00.369][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:00.369][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:00.370][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:00.401][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.402][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:00.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.403][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.416][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.416][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:00.417][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.418][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.425][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.426][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:00.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.427][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.443][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.445][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:00.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:00.447][biodb::testThat]
biodb.INFO [2025-10-11 16:02:00.453][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:00.454][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-11 16:02:00.455][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:00.455][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.457][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.458][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:02:00.467][biodb::testContext]
biodb.INFO [2025-10-11 16:02:00.468][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:00.469][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-10-11 16:02:00.470][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:00.471][biodb::testContext]
biodb.INFO [2025-10-11 16:02:00.473][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:00.474][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:00.478][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:00.479][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:00.480][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.482][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[2025-10-11 16:02:00.483][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:00.484][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.488][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:00.488][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.491][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[2025-10-11 16:02:00.492][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:00.492][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:00.493][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:00.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.496][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:00.497][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:00.498][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.500][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[2025-10-11 16:02:00.501][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:00.502][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:00.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.505][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:00.506][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:00.507][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:00.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.509][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[2025-10-11 16:02:00.510][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:00.511][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.514][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:00.515][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:00.516][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:00.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.518][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[2025-10-11 16:02:00.518][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:00.519][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:00.520][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:00.521][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:00.521][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:00.522][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:00.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.525][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:00.526][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:00.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.528][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[2025-10-11 16:02:00.529][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:00.530][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:00.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.533][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:00.538][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:00.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.541][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[2025-10-11 16:02:00.541][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:00.542][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:00.543][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:00.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.546][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:00.547][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:00.567][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:00.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.570][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[2025-10-11 16:02:00.571][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:00.571][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:00.572][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:00.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:00.576][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:00.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.578][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:02:00.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.584][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:00.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.586][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.587][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:00.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.588][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:00.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:00.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:00.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:00.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:00.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:00.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.596][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.597][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.597][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.598][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.599][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.600][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:00.601][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.602][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:00.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.605][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.606][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.608][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:00.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.610][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.610][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:00.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.612][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.613][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:00.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:00.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:00.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:00.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:00.615][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:00.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.617][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.619][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.620][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.621][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.621][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.622][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.623][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.624][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:00.625][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.626][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:02:00.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.629][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.631][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:00.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.632][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.633][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:00.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.635][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.635][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.636][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:00.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.642][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.645][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.646][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:00.647][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.648][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:00.649][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.653][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.654][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.655][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.657][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:00.658][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.659][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.660][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:00.661][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.661][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.662][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.663][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.664][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:00.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.666][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.668][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.668][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.670][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.671][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.672][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:00.673][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.674][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[2025-10-11 16:02:00.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.677][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[2025-10-11 16:02:00.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.680][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[2025-10-11 16:02:00.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.683][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[2025-10-11 16:02:00.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.686][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[2025-10-11 16:02:00.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.690][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[2025-10-11 16:02:00.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.693][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[2025-10-11 16:02:00.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.696][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[2025-10-11 16:02:00.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.700][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[2025-10-11 16:02:00.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.704][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[2025-10-11 16:02:00.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.707][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[2025-10-11 16:02:00.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.711][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[2025-10-11 16:02:00.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.714][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[2025-10-11 16:02:00.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.718][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[2025-10-11 16:02:00.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.721][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[2025-10-11 16:02:00.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.724][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[2025-10-11 16:02:00.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.728][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[2025-10-11 16:02:00.728][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:00.729][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:00.731][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:00.732][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:00.733][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:00.734][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:00.735][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:00.736][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:00.737][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:00.738][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:00.739][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:00.744][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:00.745][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:00.746][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:00.748][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:00.749][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:00.750][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:00.751][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:00.752][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:00.753][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:00.754][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:00.755][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:00.756][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:00.757][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:00.758][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:00.759][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:00.760][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:00.761][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:00.763][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:00.764][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:00.765][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:00.766][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:00.767][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:00.768][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:00.769][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:00.770][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:00.771][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:00.772][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:00.774][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:00.775][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:00.776][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:00.777][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:00.778][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:00.779][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:00.780][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:00.781][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:00.782][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:00.783][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:00.784][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:00.785][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:00.786][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:00.787][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:00.788][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:00.789][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:00.790][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:00.791][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:00.792][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:00.793][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:00.794][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:00.795][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:00.797][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:00.798][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:00.799][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:00.800][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:00.801][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:00.802][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:00.803][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:00.804][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:00.805][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:00.806][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:00.808][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:00.809][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:00.810][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:00.811][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:00.812][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:00.813][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:00.814][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:00.815][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:00.816][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:00.817][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:00.818][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:00.819][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:00.820][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:00.821][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:00.823][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:00.823][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:00.824][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.825][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.826][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[2025-10-11 16:02:00.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.835][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[2025-10-11 16:02:00.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.839][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[2025-10-11 16:02:00.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.844][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[2025-10-11 16:02:00.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.849][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[2025-10-11 16:02:00.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.854][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[2025-10-11 16:02:00.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.859][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[2025-10-11 16:02:00.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.864][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[2025-10-11 16:02:00.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.869][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[2025-10-11 16:02:00.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.873][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[2025-10-11 16:02:00.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.878][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[2025-10-11 16:02:00.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.883][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[2025-10-11 16:02:00.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.888][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[2025-10-11 16:02:00.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.893][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[2025-10-11 16:02:00.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.898][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[2025-10-11 16:02:00.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.902][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[2025-10-11 16:02:00.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:00.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:00.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:00.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:00.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:00.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:00.907][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[2025-10-11 16:02:00.909][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:00.917][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:02:00.918][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.923][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-11 16:02:00.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.925][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.927][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.928][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-11 16:02:00.929][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.930][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.930][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-11 16:02:00.931][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.932][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-11 16:02:00.932][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-11 16:02:00.933][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.933][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.934][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:00.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.936][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.939][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.940][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:00.940][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-11 16:02:00.941][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.941][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.942][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.943][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.944][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-11 16:02:00.945][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.946][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-11 16:02:00.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.950][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.952][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:00.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.953][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.954][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-11 16:02:00.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-11 16:02:00.956][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.957][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:00.958][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:00.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.963][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:00.963][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:00.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.966][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.966][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:00.967][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-11 16:02:00.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.970][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-11 16:02:00.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.974][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.975][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:00.976][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:00.977][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.977][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-11 16:02:00.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$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[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.979][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:00.980][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:00.981][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:00.981][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:00.981][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:00.982][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:00.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.983][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:00.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:00.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:00.986][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.987][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:00.987][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:00.987][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:00.988][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:00.988][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:00.989][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.990][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:00.991][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-11 16:02:00.992][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.993][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-11 16:02:00.994][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:00.995][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.997][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:00.998][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:00.999][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:00.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:01.000][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.001][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-11 16:02:01.002][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:01.002][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-11 16:02:01.002][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:01.003][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.004][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.005][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:01.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.007][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:01.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.009][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.010][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:01.010][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:01.010][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:01.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:01.015][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:01.016][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.017][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:01.017][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-11 16:02:01.019][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:01.020][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:01.021][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-11 16:02:01.022][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:01.023][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-11 16:02:01.029][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-10-11 16:02:01.095][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-10-11 16:02:01.099][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.100][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:02:01.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.102][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:01.106][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-10-11 16:02:01.107][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:01.109][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-10-11 16:02:01.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:01.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:01.128][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.131][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.135][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:01.136][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:01.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.137][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.138][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-11 16:02:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-11 16:02:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.142][ef$get] Asked field names are: location.
biodb.TRACE[2025-10-11 16:02:01.143][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-11 16:02:01.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.144][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.145][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-10-11 16:02:01.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-11 16:02:01.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.149][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-10-11 16:02:01.150][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-11 16:02:01.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.151][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.153][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-10-11 16:02:01.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-11 16:02:01.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.156][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-11 16:02:01.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:01.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.159][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.160][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-11 16:02:01.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:01.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.163][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-11 16:02:01.164][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-11 16:02:01.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.165][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-11 16:02:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-11 16:02:01.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.175][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-11 16:02:01.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:01.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:01.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:01.223][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-10-11 16:02:01.225][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:01.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:01.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.230][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:01.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:01.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:01.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:01.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:01.256][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-10-11 16:02:01.292][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:02:01.307][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-10-11 16:02:01.308][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-10-11 16:02:01.312][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:01.313][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-11 16:02:01.314][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:01.315][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:01.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:01.321][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:01.332][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.333][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:01.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.335][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:01.337][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-10-11 16:02:01.338][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-10-11 16:02:01.339][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-11 16:02:01.340][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:01.341][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:01.342][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:01.342][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:01.343][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-10-11 16:02:01.358][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.359][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:01.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.360][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:01.363][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:01.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:01.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:01.365][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:01.366][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-10-11 16:02:01.374][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-11 16:02:01.375][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:01.376][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-11 16:02:01.377][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:01.378][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:01.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:01.380][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:01.393][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:01.421][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.422][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:01.423][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.423][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:01.430][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-11 16:02:01.431][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:01.433][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-11 16:02:01.433][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:01.434][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:01.435][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:01.436][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:01.437][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:01.450][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.450][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:01.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.452][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:01.455][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-11 16:02:01.456][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:01.457][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-11 16:02:01.458][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:01.459][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:01.459][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:01.460][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:01.461][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:01.475][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.476][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:01.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.478][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.493][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.494][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:01.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.496][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.502][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.503][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:01.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.505][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.516][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.517][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:01.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:01.518][biodb::testThat]
biodb.INFO [2025-10-11 16:02:01.524][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:01.525][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-10-11 16:02:01.526][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-11 16:02:01.526][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:01.527][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.528][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.530][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:02:01.533][biodb::testContext]
biodb.INFO [2025-10-11 16:02:01.534][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:01.535][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-10-11 16:02:01.536][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:01.537][biodb::testContext]
biodb.INFO [2025-10-11 16:02:01.538][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:01.540][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:01.543][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:01.544][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:01.545][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.547][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[2025-10-11 16:02:01.547][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:01.548][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.551][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:01.552][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.554][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[2025-10-11 16:02:01.555][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:01.555][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:01.556][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:01.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.559][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:01.560][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:01.561][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.563][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[2025-10-11 16:02:01.563][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:01.564][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:01.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.567][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:01.567][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:01.569][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:01.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.575][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[2025-10-11 16:02:01.576][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:01.577][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.580][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:01.580][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:01.581][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:01.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.583][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.DEBUG[2025-10-11 16:02:01.584][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:01.585][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:01.586][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:01.587][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:01.587][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:01.588][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:01.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.591][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:01.592][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:01.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.594][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[2025-10-11 16:02:01.594][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:01.595][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:01.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.598][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:01.598][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:01.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.600][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[2025-10-11 16:02:01.601][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:01.602][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:01.603][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:01.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.605][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:01.606][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:01.624][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:01.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.626][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[2025-10-11 16:02:01.627][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:01.628][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:01.629][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:01.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:01.632][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:01.633][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.634][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:02:01.635][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.635][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:01.636][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.637][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.638][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.638][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.639][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:01.640][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:01.641][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.641][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:01.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:01.643][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:01.644][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:01.645][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:01.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.648][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:01.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.651][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:01.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:01.653][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.654][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.654][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:01.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.657][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:01.658][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:01.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.660][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.661][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.662][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:01.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:01.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.665][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:01.665][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:01.666][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.667][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.668][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:01.668][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:01.668][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:01.668][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:01.668][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:01.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:01.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.676][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:01.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.679][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:01.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:01.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.683][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:01.684][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.685][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:02:01.686][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:01.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.688][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.689][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.690][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.691][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:01.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:01.693][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.694][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:01.695][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:01.696][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.696][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.697][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.698][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:01.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.700][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:01.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.703][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.703][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:01.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:01.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.707][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.708][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:01.709][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.710][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:01.711][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:01.712][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.713][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.714][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.715][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.716][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:01.716][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:01.717][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.718][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:01.719][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:01.719][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.720][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:01.721][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.722][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:01.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:01.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:01.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:01.726][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:01.727][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:01.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:01.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:01.730][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:01.731][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:01.732][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.732][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[2025-10-11 16:02:01.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.736][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[2025-10-11 16:02:01.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.739][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[2025-10-11 16:02:01.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.743][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[2025-10-11 16:02:01.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.747][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[2025-10-11 16:02:01.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.750][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[2025-10-11 16:02:01.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.770][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[2025-10-11 16:02:01.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.775][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[2025-10-11 16:02:01.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.778][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[2025-10-11 16:02:01.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.782][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[2025-10-11 16:02:01.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.785][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[2025-10-11 16:02:01.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.789][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[2025-10-11 16:02:01.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.792][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[2025-10-11 16:02:01.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.795][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[2025-10-11 16:02:01.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.799][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[2025-10-11 16:02:01.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.802][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[2025-10-11 16:02:01.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.805][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[2025-10-11 16:02:01.806][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:01.808][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:01.809][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:01.810][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:01.811][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:01.812][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:01.814][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:01.815][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:01.816][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:01.817][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:01.818][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:01.819][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:01.820][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:01.821][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:01.823][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:01.824][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:01.825][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:01.826][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:01.827][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:01.828][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:01.829][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:01.830][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:01.832][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:01.833][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:01.834][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:01.835][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:01.836][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:01.837][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:01.838][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:01.840][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:01.841][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:01.842][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:01.843][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:01.844][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:01.845][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:01.846][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:01.848][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:01.849][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:01.850][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:01.855][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:01.856][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:01.858][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:01.859][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:01.860][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:01.861][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:01.862][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:01.863][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:01.864][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:01.865][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:01.867][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:01.868][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:01.869][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:01.870][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:01.871][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:01.872][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:01.873][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:01.875][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:01.876][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:01.877][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:01.878][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:01.879][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:01.880][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:01.881][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:01.883][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:01.884][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:01.885][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:01.886][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:01.887][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:01.888][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:01.889][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:01.890][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:01.891][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:01.892][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:01.893][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:01.895][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:01.896][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:01.897][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:01.898][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:01.899][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:01.900][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:01.902][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:01.903][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:01.904][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:01.905][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:01.907][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:01.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:01.908][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.910][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.910][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[2025-10-11 16:02:01.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.916][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[2025-10-11 16:02:01.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.921][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[2025-10-11 16:02:01.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.926][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[2025-10-11 16:02:01.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.932][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[2025-10-11 16:02:01.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.941][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[2025-10-11 16:02:01.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.947][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[2025-10-11 16:02:01.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.953][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[2025-10-11 16:02:01.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.958][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[2025-10-11 16:02:01.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.964][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[2025-10-11 16:02:01.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.969][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[2025-10-11 16:02:01.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.975][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[2025-10-11 16:02:01.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.981][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[2025-10-11 16:02:01.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.987][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[2025-10-11 16:02:01.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.992][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[2025-10-11 16:02:01.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:01.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:01.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:01.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:01.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:01.998][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[2025-10-11 16:02:01.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:01.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:02.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:02.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:02.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:02.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:02.003][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[2025-10-11 16:02:02.005][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:02.007][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:02:02.009][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.009][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-11 16:02:02.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:02.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.014][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.015][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-11 16:02:02.016][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:02.017][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.018][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-11 16:02:02.019][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:02.020][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-11 16:02:02.020][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-11 16:02:02.021][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:02.021][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:02.022][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:02.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:02.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.028][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:02.028][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-11 16:02:02.029][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:02.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:02.030][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.037][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:02.038][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-11 16:02:02.040][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.041][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-11 16:02:02.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:02.043][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.045][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.047][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:02.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:02.049][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.050][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-11 16:02:02.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-11 16:02:02.051][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-11 16:02:02.052][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:02.053][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:02.054][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:02.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:02.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.060][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:02.060][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:02.061][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:02.062][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:02.063][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.064][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:02.065][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-11 16:02:02.067][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:02.068][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-11 16:02:02.069][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:02.070][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.073][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.075][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:02.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:02.077][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.078][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-11 16:02:02.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$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[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.080][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:02.081][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:02.083][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:02.083][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:02.083][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:02.084][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:02.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:02.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.091][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:02.091][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:02.091][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:02.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:02.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:02.094][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.095][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:02.096][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-11 16:02:02.098][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.099][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-11 16:02:02.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:02.102][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.104][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.106][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:02.107][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:02.109][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.110][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-11 16:02:02.111][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:02.112][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-11 16:02:02.112][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:02.113][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:02.114][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:02.115][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:02.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.118][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:02.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:02.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:02.122][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:02.123][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:02.123][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:02.123][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:02.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:02.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:02.127][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:02.128][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:02.129][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-11 16:02:02.131][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:02.132][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:02.134][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-11 16:02:02.135][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:02.136][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-11 16:02:02.149][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-11 16:02:02.159][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-10-11 16:02:02.163][biodb::testThat]
biodb.INFO [2025-10-11 16:02:02.164][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:02:02.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:02.166][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:02.168][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-10-11 16:02:02.170][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:02.173][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-11 16:02:02.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:02.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:02.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:02.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:02.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:02.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:02.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:02.189][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.190][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.192][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.199][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.201][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.203][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.210][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.211][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.213][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.215][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.220][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.221][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.223][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.229][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.230][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.232][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.239][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.240][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.243][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.248][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:02.248][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.250][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.251][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.255][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.256][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.257][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.258][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.268][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.269][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.270][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.275][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.277][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.282][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.283][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.285][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.286][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.289][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:02.290][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.291][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:02.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.295][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.296][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.298][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.302][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.303][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.305][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.309][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-11 16:02:02.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-11 16:02:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.329][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-11 16:02:02.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.337][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-11 16:02:02.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.348][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.351][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-11 16:02:02.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.373][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:02.395][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-10-11 16:02:02.397][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.400][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:02.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:02.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.403][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:02.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:02.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.407][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:02.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:02.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.413][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:02.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:02.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.417][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:02.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.460][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:02.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.485][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.485][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.487][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.498][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:02.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.511][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:02.512][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.514][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.515][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:02.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:02.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.535][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:02.535][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.537][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:02.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.557][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.560][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.571][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.574][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.577][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.580][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.581][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.582][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.583][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.607][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.608][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.609][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.610][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.620][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.631][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.631][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.633][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.634][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.650][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.653][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.654][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.655][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.666][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.669][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.676][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.679][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.680][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.681][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.682][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.701][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.702][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.704][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.704][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.724][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.725][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.727][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.738][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.746][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.747][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.749][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.750][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.774][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.776][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.797][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.798][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.799][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.821][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.821][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.823][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.834][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.835][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.836][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.845][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.846][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.848][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.852][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.853][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.855][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.859][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.860][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.862][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.866][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.867][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:02.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.869][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.873][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.874][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:02.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.876][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.880][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:02.881][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:02.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.883][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.888][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:02.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:02.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.890][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:02.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.897][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.901][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:02.902][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:02.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.904][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.908][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.909][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:02.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.910][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.914][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.915][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:02.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.917][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.921][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:02.921][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:02.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.923][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.927][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.928][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:02.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.929][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.938][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.939][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:02.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.941][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.946][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-10-11 16:02:02.947][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:02.948][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-11 16:02:02.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:02.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:02.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:02.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:02.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:02.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:02.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:02.959][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.960][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.962][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:02.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:02.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.979][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.980][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.981][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.985][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.986][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.988][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:02.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.992][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.993][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.994][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.995][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:02.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:02.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:02.999][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.000][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.001][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.006][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.006][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.008][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.016][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:03.017][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.019][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-11 16:02:03.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.023][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.025][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.029][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.032][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.036][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.037][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.038][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.042][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.043][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.044][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.046][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.049][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:03.049][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.051][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-11 16:02:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.055][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.056][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.057][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.058][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.061][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.062][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.064][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.068][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-11 16:02:03.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.071][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.074][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.077][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-11 16:02:03.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.086][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-11 16:02:03.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.096][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-11 16:02:03.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.105][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.108][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-11 16:02:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.121][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.124][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.130][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:03.151][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-10-11 16:02:03.153][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.159][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:03.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:03.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.166][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:03.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:03.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:03.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:03.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:03.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:03.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.176][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:03.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:03.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.187][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.216][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.219][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.222][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:03.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.241][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.243][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.272][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.275][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.295][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.298][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.319][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.320][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.321][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.332][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.339][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.342][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.345][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.346][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.348][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.349][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.359][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.365][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.368][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.369][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.370][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.392][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.393][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.394][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.416][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.422][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.444][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.445][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.446][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.468][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.469][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.471][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.492][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.493][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.495][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.530][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.531][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.532][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.583][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.589][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.590][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.592][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.607][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.614][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.615][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.617][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.617][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.649][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.650][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.651][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:03.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:03.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.666][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.671][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.672][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-11 16:02:03.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.673][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.678][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.679][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-11 16:02:03.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.680][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.685][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.686][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-11 16:02:03.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.687][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.692][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.693][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-11 16:02:03.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.694][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.699][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.700][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-11 16:02:03.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.701][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.706][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:03.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:03.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.709][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.713][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:03.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:03.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.716][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.720][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.721][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:03.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.723][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.728][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-11 16:02:03.728][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-11 16:02:03.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.730][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.735][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.735][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.737][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.747][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-11 16:02:03.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.749][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.754][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.755][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.756][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.761][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.762][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-11 16:02:03.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.764][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.768][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.769][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-11 16:02:03.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.771][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:03.778][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.779][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:03.780][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.781][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:03.782][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:03.785][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:03.787][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:03.788][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:03.788][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:03.789][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:03.790][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:03.791][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-11 16:02:03.802][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.803][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:03.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.804][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:03.807][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.809][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:03.810][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-10-11 16:02:03.819][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-11 16:02:03.820][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:03.821][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:03.822][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:03.823][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:03.823][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:03.824][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:03.825][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:03.841][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.842][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:03.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.843][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:03.850][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-11 16:02:03.851][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:03.852][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:03.853][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:03.854][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:03.855][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:03.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:03.856][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:03.867][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.868][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:03.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.870][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:03.873][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-11 16:02:03.874][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:03.876][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:03.876][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:03.877][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:03.878][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:03.879][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:03.880][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:03.891][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.892][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:03.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.894][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.906][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.907][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:03.908][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.909][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.926][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.927][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:03.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.928][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.940][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.941][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:03.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.943][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:03.961][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:03.962][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:03.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.964][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:03.965][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:03.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:03.967][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:03.969][biodb::testThat]
biodb.INFO [2025-10-11 16:02:03.969][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-10-11 16:02:03.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:03.971][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:03.977][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-11 16:02:03.978][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:03.979][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:03.980][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:03.981][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:03.982][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:03.983][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:03.984][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:04.000][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.001][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-10-11 16:02:04.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.002][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:04.005][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:04.006][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:04.007][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:04.008][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:04.009][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.010][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:04.010][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:04.011][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-11 16:02:04.023][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.023][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-10-11 16:02:04.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.025][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:04.028][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:04.029][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:04.030][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:04.031][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:04.032][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.033][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:04.033][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:04.034][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-11 16:02:04.046][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.047][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-10-11 16:02:04.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.049][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:04.051][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:04.052][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:04.053][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:04.054][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:04.055][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.056][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:04.057][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:04.057][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.TRACE[2025-10-11 16:02:04.069][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:04.070][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:04.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.071][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.072][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:04.073][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:04.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.074][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:04.080][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.081][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-10-11 16:02:04.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.082][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:04.085][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:04.086][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:04.087][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:04.088][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:04.088][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:04.090][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:04.091][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-11 16:02:04.102][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.103][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-10-11 16:02:04.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.105][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:04.107][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-11 16:02:04.108][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-11 16:02:04.109][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:04.110][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:04.111][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.112][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:04.113][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:04.114][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-11 16:02:04.125][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:04.126][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-10-11 16:02:04.127][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:04.128][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.129][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.131][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:02:04.135][biodb::testContext]
biodb.INFO [2025-10-11 16:02:04.135][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:04.136][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-10-11 16:02:04.137][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:04.138][biodb::testContext]
biodb.INFO [2025-10-11 16:02:04.140][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:04.141][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:04.145][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:04.145][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:04.146][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.148][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[2025-10-11 16:02:04.149][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:04.150][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.153][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:04.154][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.156][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[2025-10-11 16:02:04.157][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:04.157][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:04.158][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:04.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.166][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:04.167][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:04.167][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.170][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[2025-10-11 16:02:04.170][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:04.171][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:04.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.175][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:04.175][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:04.176][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:04.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.179][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[2025-10-11 16:02:04.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:04.180][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:04.184][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:04.185][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:04.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.188][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[2025-10-11 16:02:04.189][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:04.189][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:04.190][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:04.191][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:04.192][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:04.193][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:04.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.196][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:04.197][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:04.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.199][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[2025-10-11 16:02:04.200][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:04.201][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:04.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.204][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:04.205][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:04.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.207][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[2025-10-11 16:02:04.208][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:04.208][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:04.209][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:04.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.212][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:04.213][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:04.234][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:04.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.237][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[2025-10-11 16:02:04.238][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:04.238][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:04.239][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:04.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:04.242][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:04.244][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.245][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:02:04.245][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.246][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.247][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.248][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:04.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.253][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:04.253][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.254][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.255][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.256][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:04.256][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:04.256][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:04.256][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:04.256][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:04.257][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:04.258][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.264][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.266][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.267][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.269][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.270][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.271][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:04.272][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.273][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:04.274][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.275][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.276][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.276][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.279][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:04.280][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.281][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.281][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:04.282][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.283][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.284][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.285][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:04.285][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:04.285][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:04.285][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:04.285][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:04.286][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:04.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.288][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.290][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.291][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.292][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.293][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.294][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.294][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.295][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:04.297][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.298][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:02:04.299][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.303][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:04.304][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.305][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.306][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:04.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.308][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.308][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.309][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.310][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:04.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.316][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.319][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.320][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:04.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.322][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:04.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.328][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:04.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.330][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.330][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:04.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.332][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.333][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.334][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:04.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.345][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.347][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.348][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:04.350][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.350][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[2025-10-11 16:02:04.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.354][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[2025-10-11 16:02:04.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.358][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[2025-10-11 16:02:04.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.361][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[2025-10-11 16:02:04.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.365][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[2025-10-11 16:02:04.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.369][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[2025-10-11 16:02:04.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.372][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[2025-10-11 16:02:04.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.376][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[2025-10-11 16:02:04.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.380][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[2025-10-11 16:02:04.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.383][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[2025-10-11 16:02:04.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.387][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[2025-10-11 16:02:04.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.390][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[2025-10-11 16:02:04.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.394][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[2025-10-11 16:02:04.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.397][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[2025-10-11 16:02:04.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.401][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[2025-10-11 16:02:04.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.404][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[2025-10-11 16:02:04.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.407][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[2025-10-11 16:02:04.408][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:04.409][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:04.410][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:04.412][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:04.417][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:04.418][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:04.420][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:04.421][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:04.422][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:04.423][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:04.424][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:04.425][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:04.427][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:04.428][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:04.429][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:04.430][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:04.431][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:04.433][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:04.434][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:04.435][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:04.436][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:04.437][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:04.438][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:04.439][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:04.441][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:04.442][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:04.443][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:04.444][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:04.445][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:04.446][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:04.447][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:04.448][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:04.449][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:04.450][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:04.452][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:04.453][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:04.454][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:04.455][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:04.456][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:04.457][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:04.459][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:04.460][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:04.461][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:04.462][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:04.463][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:04.464][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:04.465][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:04.466][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:04.467][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:04.469][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:04.470][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:04.471][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:04.472][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:04.473][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:04.474][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:04.475][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:04.476][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:04.477][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:04.478][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:04.479][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:04.481][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:04.482][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:04.483][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:04.484][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:04.485][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:04.486][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:04.492][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:04.493][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:04.494][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:04.495][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:04.496][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:04.497][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:04.498][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:04.500][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:04.501][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:04.502][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:04.503][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:04.504][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:04.505][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:04.506][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:04.507][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:04.509][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:04.510][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:04.511][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:04.512][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-11 16:02:04.513][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:04.514][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.515][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.516][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[2025-10-11 16:02:04.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.521][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[2025-10-11 16:02:04.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.526][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[2025-10-11 16:02:04.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.531][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[2025-10-11 16:02:04.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.536][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[2025-10-11 16:02:04.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.542][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[2025-10-11 16:02:04.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.547][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[2025-10-11 16:02:04.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.552][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[2025-10-11 16:02:04.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.556][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[2025-10-11 16:02:04.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.561][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[2025-10-11 16:02:04.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.571][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[2025-10-11 16:02:04.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.576][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[2025-10-11 16:02:04.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.581][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[2025-10-11 16:02:04.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.586][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[2025-10-11 16:02:04.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.591][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[2025-10-11 16:02:04.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.596][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[2025-10-11 16:02:04.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:04.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.600][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[2025-10-11 16:02:04.602][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:04.610][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-11 16:02:04.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.613][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-11 16:02:04.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.616][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.617][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.618][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-11 16:02:04.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.621][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-11 16:02:04.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.622][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-11 16:02:04.622][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-11 16:02:04.623][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.624][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.625][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:04.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.627][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.630][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-11 16:02:04.630][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-11 16:02:04.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.632][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.633][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.634][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-11 16:02:04.640][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.641][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-11 16:02:04.642][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.645][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.646][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:04.647][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.648][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.649][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-11 16:02:04.650][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-11 16:02:04.651][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.652][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:04.653][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:04.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.659][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.659][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:04.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.661][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.662][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.663][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-11 16:02:04.664][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.665][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-11 16:02:04.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.669][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.671][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:04.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.672][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.673][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-11 16:02:04.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$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[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.675][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-11 16:02:04.676][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:04.677][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:04.677][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:04.678][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:04.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.682][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.683][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.683][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:04.683][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:04.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.686][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.686][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:04.687][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-11 16:02:04.689][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.690][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-11 16:02:04.691][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.691][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:04.692][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.693][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.694][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.695][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-11 16:02:04.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:04.697][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.698][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-11 16:02:04.698][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:04.699][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-11 16:02:04.699][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-11 16:02:04.700][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:04.700][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:04.701][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-11 16:02:04.702][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.703][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.703][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:04.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:04.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:04.706][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:04.707][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:04.707][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-11 16:02:04.707][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-11 16:02:04.707][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:04.708][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:04.709][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:04.710][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-11 16:02:04.716][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-11 16:02:04.717][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:04.719][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:04.720][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-11 16:02:04.721][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:04.722][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-11 16:02:04.727][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-11 16:02:04.734][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-10-11 16:02:04.737][biodb::testThat]
biodb.INFO [2025-10-11 16:02:04.738][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:02:04.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:04.740][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:04.742][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-10-11 16:02:04.743][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:04.746][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-10-11 16:02:04.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:04.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:04.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:04.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:04.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:04.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:04.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:04.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.760][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.765][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:04.765][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:04.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.767][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:04.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.772][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.775][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:04.810][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-10-11 16:02:04.812][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:04.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:04.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.815][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-11 16:02:04.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-11 16:02:04.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:04.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-11 16:02:04.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:04.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:04.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.825][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:04.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:04.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.828][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:04.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:04.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.832][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:04.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:04.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.842][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:04.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:04.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:04.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:04.871][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:04.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:05.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:05.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-11 16:02:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.028][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.030][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.050][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.051][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.052][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.063][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:05.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:05.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.065][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:05.070][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.070][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-11 16:02:05.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:05.072][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:05.079][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.080][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:05.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.082][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:05.083][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-11 16:02:05.087][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:05.088][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:05.089][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:05.089][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:05.090][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:05.091][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:05.092][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:05.103][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.104][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:05.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.105][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.111][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.112][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:05.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.114][biodb::testThat]
biodb.WARN [2025-10-11 16:02:05.117][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-11 16:02:05.121][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-11 16:02:05.129][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.130][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:05.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.132][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:05.135][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-11 16:02:05.136][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-11 16:02:05.137][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-11 16:02:05.138][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-11 16:02:05.139][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:05.140][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-11 16:02:05.140][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-11 16:02:05.141][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-11 16:02:05.154][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.155][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:05.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.156][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.169][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.170][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:05.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.172][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.185][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.186][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:05.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.188][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.202][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.203][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:05.204][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:05.205][biodb::testThat]
biodb.INFO [2025-10-11 16:02:05.218][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:05.219][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-10-11 16:02:05.220][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:05.221][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:05.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:05.223][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:05.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:05.224][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:05.225][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 0 | PASS 247 ]

══ 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 0 | PASS 247 ]
Error: Test failures
In addition: 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_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.13.1’
* 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’ ... WARNING
'library' or 'require' call not declared from: ‘biodbNci’
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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 0 | PASS 247 ]
  Error: Test failures
  In addition: 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, 1 WARNING, 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 ‘1.13.1’
** 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)