Back to Long Tests report for BioC 3.22

This page was generated on 2026-04-04 23:55 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4691
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 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-04-04 09:55 -0400 (Sat, 04 Apr 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on merida1

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-04-04 16:01:13 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 16:02:34 -0400 (Sat, 04 Apr 2026)
EllapsedTime: 81.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-04-04 16:02:30.401][biodb::testContext]
biodb.INFO [2026-04-04 16:02:30.405][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:30.406][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-04-04 16:02:30.408][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:30.409][biodb::testContext]
biodb.INFO [2026-04-04 16:02:30.416][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:30.418][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:30.426][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:30.427][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:30.429][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.433][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:30.458][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.462][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:30.464][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.468][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:30.470][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:30.471][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:30.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.476][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:30.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:30.479][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.483][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:30.485][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:30.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.489][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:30.491][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:30.492][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:30.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.497][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:30.498][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.503][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:30.504][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:30.506][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:30.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.510][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:30.512][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:30.513][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:30.514][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:30.516][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:30.517][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:30.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.522][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:30.523][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:30.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.528][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:30.529][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:30.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.534][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:30.535][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:30.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.540][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:30.541][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:30.542][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:30.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.547][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:30.549][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:30.559][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:30.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.564][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:30.566][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:30.567][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:30.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.570][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[2026-04-04 16:02:30.574][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:30.620][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.649][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:02:30.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:30.654][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.655][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.658][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.659][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:30.660][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:30.661][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.663][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:30.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:30.665][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.666][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.668][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:30.668][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:30.668][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:30.668][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:30.668][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:30.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:30.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:30.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.677][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:30.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:30.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.684][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:30.686][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.687][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:30.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.690][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:30.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.693][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:30.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:30.698][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.700][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:30.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:30.702][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:30.705][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:30.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:30.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:30.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.714][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:30.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:30.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.719][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.721][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:30.723][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.724][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:02:30.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:30.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.733][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:30.734][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:30.735][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.736][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:30.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:30.739][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.742][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.743][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:30.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:30.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.751][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:30.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:30.755][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.756][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.757][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:30.760][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.761][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:30.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:30.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.770][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:30.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:30.772][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.773][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:30.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:30.776][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:30.778][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:30.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:30.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:30.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:30.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:30.788][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.789][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:30.790][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:30.791][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:30.793][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:30.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:30.798][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.799][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[2026-04-04 16:02:30.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.844][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[2026-04-04 16:02:30.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.878][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[2026-04-04 16:02:30.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:30.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:30.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:30.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:30.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:30.891][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:30.896][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:30.898][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:30.904][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:30.906][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:30.908][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:30.910][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:30.912][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:30.914][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:30.915][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:30.917][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:30.919][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:30.921][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:30.923][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:30.925][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:30.927][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:30.928][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:30.930][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:30.932][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:30.935][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:30.937][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:30.939][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:30.941][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:30.944][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:30.946][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:30.948][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:30.950][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:30.952][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:30.954][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:30.956][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:30.958][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:30.960][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:30.961][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:30.963][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:30.965][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:30.967][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:30.969][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:30.971][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:30.973][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:30.975][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:30.976][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:30.978][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:30.980][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:30.982][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:30.984][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:30.985][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:30.987][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:30.989][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:30.991][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:30.992][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:30.994][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:30.996][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:30.997][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:30.999][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:31.001][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:31.002][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:31.004][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:31.006][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:31.008][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:31.009][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:31.011][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:31.013][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:31.014][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:31.016][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:31.018][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:31.019][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:31.021][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:31.023][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:31.024][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:31.026][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:31.028][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:31.030][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:31.031][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:31.033][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:31.035][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:31.036][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:31.038][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:31.040][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:31.041][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:31.043][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:31.045][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:31.047][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:31.048][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:31.056][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:31.058][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:31.061][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:31.062][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.065][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.118][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[2026-04-04 16:02:31.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.125][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[2026-04-04 16:02:31.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.148][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[2026-04-04 16:02:31.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.156][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[2026-04-04 16:02:31.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.168][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[2026-04-04 16:02:31.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.183][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[2026-04-04 16:02:31.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:31.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.199][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[2026-04-04 16:02:31.201][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:31.214][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-04-04 16:02:31.216][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:31.218][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-04-04 16:02:31.219][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:31.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:31.221][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:31.223][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-04-04 16:02:31.224][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:31.225][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:31.226][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-04-04 16:02:31.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:31.229][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:31.230][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-04-04 16:02:31.231][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-04-04 16:02:31.232][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-04-04 16:02:31.234][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:31.235][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:31.236][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:31.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:31.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:31.240][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:31.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:31.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:31.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:31.245][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:31.245][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:31.245][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-04-04 16:02:31.245][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-04-04 16:02:31.246][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:31.247][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:31.248][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:31.249][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:31.257][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-04-04 16:02:31.279][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-04-04 16:02:31.294][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-04-04 16:02:31.303][biodb::testThat]
biodb.INFO [2026-04-04 16:02:31.304][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:31.306][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:31.307][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:31.311][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-04-04 16:02:31.313][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:31.316][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-04-04 16:02:31.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:31.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:31.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:31.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:31.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:31.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:31.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.484][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.489][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:31.579][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-04-04 16:02:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:31.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.597][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:31.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:31.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.674][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.684][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:31.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.714][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.716][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.717][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.751][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.753][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.754][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.788][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.790][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.791][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.792][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.827][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.828][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.829][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.863][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.866][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.867][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.892][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:31.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:31.895][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.897][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.904][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:31.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:31.907][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.908][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:31.917][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:31.918][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.920][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.927][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.929][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:31.930][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.931][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.938][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:31.941][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:31.942][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:31.966][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-04-04 16:02:32.013][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:32.015][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-04-04 16:02:32.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:32.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:32.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:32.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:32.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:32.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:32.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:02:32.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.079][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.084][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.095][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.204][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.209][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.219][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:32.255][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-04-04 16:02:32.282][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:32.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:32.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.287][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:32.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:32.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.292][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:32.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:32.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:32.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.315][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:02:32.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.414][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.416][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.418][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.434][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.439][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.444][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.449][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.451][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.452][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.453][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.454][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.485][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.487][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.488][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.489][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.522][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.523][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.524][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.525][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.558][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.560][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.561][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.598][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.601][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.602][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.637][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.638][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.639][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.657][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:32.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:32.660][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.661][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.668][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.669][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:32.671][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.672][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.679][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:32.680][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:32.681][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.683][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.689][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:32.691][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:32.692][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.693][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.701][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:32.703][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.704][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.711][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.712][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:02:32.713][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.715][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:32.721][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:32.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:32.724][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:32.725][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:32.736][biodb::testThat]
biodb.INFO [2026-04-04 16:02:32.738][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:32.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:32.740][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:32.743][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-04-04 16:02:32.749][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-04-04 16:02:32.752][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:32.793][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-04-04 16:02:32.795][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-04-04 16:02:32.796][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-04-04 16:02:32.979][biodb::testThat]
biodb.INFO [2026-04-04 16:02:32.981][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:32.982][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:32.983][biodb::testThat]
biodb.INFO [2026-04-04 16:02:32.992][biodb::testThat]
biodb.INFO [2026-04-04 16:02:32.993][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:32.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:32.996][biodb::testThat]
biodb.WARN [2026-04-04 16:02:33.025][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-04-04 16:02:33.050][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-04-04 16:02:33.060][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.062][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:33.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:33.064][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:33.088][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-04-04 16:02:33.153][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:33.156][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:33.157][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-04-04 16:02:33.159][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-04-04 16:02:33.177][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-04-04 16:02:33.253][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.255][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:33.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:33.257][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.267][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.268][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:33.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:33.271][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.281][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.283][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:33.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:33.285][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.294][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.295][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:33.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:33.298][biodb::testThat]
biodb.INFO [2026-04-04 16:02:33.306][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:33.308][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-04-04 16:02:33.309][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:33.310][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.312][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.314][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-04-04 16:02:33.329][biodb::testContext]
biodb.INFO [2026-04-04 16:02:33.330][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:33.331][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-04-04 16:02:33.332][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:33.334][biodb::testContext]
biodb.INFO [2026-04-04 16:02:33.336][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:33.338][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:33.342][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:33.344][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:33.345][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.349][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[2026-04-04 16:02:33.350][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:33.351][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.356][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:33.357][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.362][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:33.363][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:33.364][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:33.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.369][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:33.370][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:33.372][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.376][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:33.377][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:33.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.382][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:33.383][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:33.385][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:33.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.389][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:33.391][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.395][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:33.396][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:33.398][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:33.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.401][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[2026-04-04 16:02:33.407][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:33.408][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:33.409][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:33.411][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:33.412][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:33.413][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:33.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.418][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:33.419][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:33.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.423][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:33.425][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:33.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.429][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:33.431][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:33.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.435][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:33.436][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:33.438][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:33.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.442][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:33.444][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:33.454][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:33.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.459][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:33.460][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:33.462][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:33.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.467][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:33.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.470][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:02:33.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:33.474][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.475][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.476][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.479][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:33.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:33.482][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.483][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:33.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:33.485][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.487][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.488][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:33.488][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:33.488][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:33.488][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:33.488][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:33.489][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:33.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.493][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:33.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.496][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.498][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.499][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:33.500][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:33.501][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.502][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.504][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:33.506][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.507][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:33.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.510][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:33.511][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.512][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.514][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.515][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.516][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:33.517][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:33.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.520][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:33.521][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:33.522][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.525][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:33.525][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:33.525][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:33.525][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:33.525][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:33.526][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:33.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:33.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.534][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.535][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:33.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:33.538][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.540][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.541][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:33.543][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.545][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:02:33.546][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.547][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:33.548][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.550][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.551][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.552][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.554][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:33.555][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:33.556][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.558][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:33.559][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:33.560][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.563][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.564][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:33.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:33.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.572][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:33.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:33.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.577][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.578][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:33.580][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.582][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:33.583][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.584][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:33.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.591][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:33.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:33.594][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.595][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:33.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:33.597][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.599][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:33.600][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:33.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.605][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:33.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:33.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:33.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:33.610][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:33.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:33.618][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:33.619][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:33.620][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:33.622][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.690][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[2026-04-04 16:02:33.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.696][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[2026-04-04 16:02:33.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.707][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[2026-04-04 16:02:33.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.714][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:33.716][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:33.717][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:33.719][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:33.721][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:33.723][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:33.724][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:33.726][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:33.728][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:33.729][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:33.731][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:33.733][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:33.735][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:33.736][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:33.738][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:33.740][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:33.741][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:33.743][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:33.745][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:33.747][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:33.748][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:33.750][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:33.752][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:33.753][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:33.755][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:33.757][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:33.759][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:33.760][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:33.762][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:33.764][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:33.765][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:33.767][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:33.769][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:33.771][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:33.772][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:33.774][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:33.776][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:33.777][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:33.779][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:33.781][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:33.782][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:33.784][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:33.786][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:33.787][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:33.789][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:33.791][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:33.793][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:33.794][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:33.796][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:33.798][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:33.799][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:33.801][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:33.807][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:33.809][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:33.811][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:33.812][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:33.814][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:33.816][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:33.817][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:33.819][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:33.821][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:33.822][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:33.824][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:33.826][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:33.827][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:33.829][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:33.831][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:33.833][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:33.834][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:33.836][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:33.838][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:33.839][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:33.841][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:33.843][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:33.844][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:33.846][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:33.848][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:33.850][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:33.851][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:33.853][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:33.855][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:33.856][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:33.858][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:33.860][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:33.862][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:33.863][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:33.864][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.866][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.898][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[2026-04-04 16:02:33.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.929][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[2026-04-04 16:02:33.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.945][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[2026-04-04 16:02:33.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.969][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[2026-04-04 16:02:33.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:33.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:33.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:33.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:33.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:33.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:33.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:33.992][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[2026-04-04 16:02:33.999][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:34.001][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-04-04 16:02:34.004][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:34.005][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-04-04 16:02:34.006][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:34.007][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:34.009][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:34.010][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-04-04 16:02:34.011][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:34.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:34.014][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-04-04 16:02:34.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:34.016][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:34.017][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-04-04 16:02:34.019][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-04-04 16:02:34.020][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-04-04 16:02:34.021][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:34.023][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:34.024][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:34.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:34.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:34.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:34.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:34.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:34.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:34.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:34.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:02:34.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-04-04 16:02:34.032][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-04-04 16:02:34.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:34.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:34.036][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:34.037][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:34.039][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-04-04 16:02:34.043][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-04-04 16:02:34.047][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-04-04 16:02:34.049][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:34.050][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-04-04 16:02:34.051][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:34.052][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:34.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:34.055][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:34.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:34.057][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:34.058][FUN] Functions in observer 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 2 | WARN 0 | SKIP 2 | PASS 85 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
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 biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)