Back to Long Tests report for BioC 3.21

This page was generated on 2025-10-04 23:55 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
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 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-04 09:55 -0400 (Sat, 04 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo1

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: 1.12.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
StartedAt: 2025-10-04 16:02:30 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 16:03:32 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 62.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-10-04 16:03:28.455][biodb::testContext]
biodb.INFO [2025-10-04 16:03:28.457][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:28.458][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-04 16:03:28.459][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:28.460][biodb::testContext]
biodb.INFO [2025-10-04 16:03:28.466][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:03:28.468][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:28.475][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:28.476][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:03:28.477][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.481][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:03:28.498][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.501][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[2025-10-04 16:03:28.502][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:03:28.503][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.516][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:03:28.517][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:03:28.518][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:03:28.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.520][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[2025-10-04 16:03:28.521][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:03:28.522][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:03:28.523][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.527][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:03:28.528][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:03:28.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.531][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:03:28.532][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:03:28.533][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:03:28.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.536][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:03:28.537][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.541][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:03:28.542][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:03:28.543][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:03:28.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.546][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:28.547][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:03:28.548][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:03:28.549][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:03:28.550][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:03:28.551][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:03:28.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.555][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:03:28.556][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:03:28.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.559][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:03:28.560][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:03:28.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.564][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:03:28.565][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:03:28.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.568][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:03:28.569][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:03:28.570][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:03:28.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.573][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:28.574][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:03:28.580][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:03:28.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.583][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:03:28.584][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:03:28.585][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:03:28.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.591][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:03:28.622][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:03:28.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:28.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.644][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:28.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:28.646][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.647][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:03:28.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:28.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.650][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:28.650][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:28.650][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:28.650][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:28.650][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:28.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:28.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:28.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.657][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.658][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:28.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:28.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.661][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.663][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:03:28.664][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.665][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:28.666][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:28.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.669][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.670][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.677][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:28.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:28.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.679][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:03:28.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:28.681][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.683][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:28.683][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:28.683][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:28.683][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:28.683][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:28.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:28.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:28.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.691][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:28.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:28.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.694][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.695][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:03:28.697][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.698][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:03:28.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:28.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.705][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:28.706][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:28.707][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.708][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:03:28.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:28.710][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.711][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:28.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:28.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.719][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.720][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:28.721][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:28.721][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.722][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.724][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:03:28.725][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.726][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:28.727][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.728][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:28.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.732][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.733][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:28.734][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:28.735][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.736][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:03:28.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:28.738][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.739][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:28.740][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.741][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:28.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.743][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:28.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:28.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:28.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:28.747][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:28.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:28.750][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:28.751][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:28.754][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:28.755][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.816][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[2025-10-04 16:03:28.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.835][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:03:28.842][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:03:28.843][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:03:28.862][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:03:28.864][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:03:28.865][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:03:28.867][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:28.868][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:28.870][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:03:28.871][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:03:28.873][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:03:28.874][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:03:28.876][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:28.877][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:28.878][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:03:28.880][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:03:28.882][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:03:28.883][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:03:28.885][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:03:28.886][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:03:28.887][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:03:28.889][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:03:28.890][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:03:28.892][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:03:28.893][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:03:28.895][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:03:28.896][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:03:28.897][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:03:28.899][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:03:28.900][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:03:28.902][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:03:28.903][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:03:28.905][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:03:28.906][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:03:28.908][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:03:28.909][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:03:28.910][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:03:28.912][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:03:28.913][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:03:28.915][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:03:28.916][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:03:28.917][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:03:28.919][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:03:28.920][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:03:28.922][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:03:28.923][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:03:28.925][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:03:28.926][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:03:28.928][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:03:28.929][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:03:28.930][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:03:28.932][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:03:28.933][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:03:28.935][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:03:28.936][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:03:28.937][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:03:28.939][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:03:28.940][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:03:28.942][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:03:28.943][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:03:28.945][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:03:28.946][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:03:28.947][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:03:28.949][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:03:28.950][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:03:28.952][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:03:28.953][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:03:28.955][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:03:28.956][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:03:28.957][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:03:28.959][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:03:28.960][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:03:28.962][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:03:28.963][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:03:28.964][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:03:28.966][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:03:28.967][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:03:28.969][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:03:28.970][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:03:28.972][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:03:28.973][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:03:28.974][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:03:28.976][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:03:28.982][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:03:28.984][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:03:28.987][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:28.988][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:28.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:28.990][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:28.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:28.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:28.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:28.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:28.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.066][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[2025-10-04 16:03:29.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:29.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:29.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.095][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[2025-10-04 16:03:29.097][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:29.106][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:29.108][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:29.109][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-04 16:03:29.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:29.111][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:29.112][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:29.113][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-04 16:03:29.114][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:29.115][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:29.116][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-04 16:03:29.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:29.118][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:29.118][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-04 16:03:29.119][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-04 16:03:29.120][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-04 16:03:29.121][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:29.122][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:29.123][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:03:29.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:29.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:29.126][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:29.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:29.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:29.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:29.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:29.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:29.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-04 16:03:29.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-04 16:03:29.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:29.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:29.132][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:29.133][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:29.139][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-04 16:03:29.160][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:29.175][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-04 16:03:29.183][biodb::testThat]
biodb.INFO [2025-10-04 16:03:29.184][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:03:29.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:29.186][biodb::testThat]
biodb.TRACE[2025-10-04 16:03:29.195][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-04 16:03:29.197][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:03:29.200][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-04 16:03:29.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:03:29.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:03:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.332][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:03:29.388][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-04 16:03:29.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:29.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:29.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:29.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.421][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.494][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.502][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.523][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.525][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.548][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.549][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.551][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.573][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.576][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.602][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.603][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.605][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.627][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.628][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.630][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.644][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.648][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.650][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.654][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.657][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.661][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.662][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.664][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.667][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.670][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.686][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-04 16:03:29.723][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:03:29.724][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-04 16:03:29.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:03:29.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:29.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:29.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:29.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:29.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:29.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:03:29.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:29.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:29.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:29.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:29.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:29.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:29.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:29.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.839][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.843][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.850][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:03:29.877][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-04 16:03:29.897][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:03:29.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:29.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:03:29.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:29.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:03:29.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.920][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.955][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.958][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.962][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-04 16:03:29.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.992][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.993][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.995][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:29.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:29.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:29.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:29.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.006][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.010][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.017][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.018][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.020][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.021][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.042][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.045][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.071][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.072][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.074][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.075][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.096][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.097][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.099][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.122][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.124][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.147][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.148][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.149][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.161][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:03:30.162][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:03:30.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.163][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.167][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.168][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-04 16:03:30.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.170][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.174][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:03:30.179][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:03:30.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.180][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:03:30.185][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:03:30.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.187][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.191][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.192][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:03:30.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.194][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.198][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.199][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:03:30.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.200][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:03:30.204][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:03:30.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:03:30.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:03:30.207][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:03:30.213][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.214][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:03:30.215][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.216][biodb::testThat]
biodb.DEBUG[2025-10-04 16:03:30.218][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-04 16:03:30.220][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-04 16:03:30.222][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-04 16:03:30.250][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-04 16:03:30.251][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-04 16:03:30.252][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-04 16:03:30.294][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.295][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:03:30.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.296][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.302][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.302][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:03:30.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.304][biodb::testThat]
biodb.WARN [2025-10-04 16:03:30.322][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-04 16:03:30.340][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-04 16:03:30.347][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.348][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:03:30.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.350][biodb::testThat]
biodb.DEBUG[2025-10-04 16:03:30.366][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-04 16:03:30.414][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-04 16:03:30.415][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-04 16:03:30.416][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-04 16:03:30.417][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-04 16:03:30.429][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-04 16:03:30.451][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.452][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:03:30.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.454][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.460][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.461][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:03:30.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.463][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.469][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.470][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:03:30.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.472][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.477][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.478][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:03:30.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:03:30.480][biodb::testThat]
biodb.INFO [2025-10-04 16:03:30.485][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:03:30.486][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-04 16:03:30.487][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:03:30.491][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.493][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.495][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-04 16:03:30.504][biodb::testContext]
biodb.INFO [2025-10-04 16:03:30.505][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:30.506][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-04 16:03:30.507][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:03:30.508][biodb::testContext]
biodb.INFO [2025-10-04 16:03:30.510][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:03:30.511][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:30.515][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:30.516][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:03:30.517][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.520][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:03:30.521][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.525][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:03:30.526][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.529][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:03:30.530][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:03:30.531][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:03:30.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.535][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:03:30.536][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:03:30.537][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.540][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:03:30.541][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:03:30.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.545][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:03:30.546][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:03:30.547][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:03:30.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.550][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:03:30.551][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.554][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:03:30.555][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:03:30.556][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:03:30.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.560][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:30.561][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:03:30.562][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:03:30.563][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:03:30.564][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:03:30.565][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:03:30.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.568][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:03:30.569][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:03:30.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.573][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:03:30.574][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:03:30.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.577][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:03:30.578][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:03:30.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.581][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:03:30.582][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:03:30.583][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:03:30.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.587][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:03:30.588][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:03:30.591][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:03:30.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.594][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:03:30.595][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:03:30.596][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:03:30.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.600][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:03:30.602][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.607][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:03:30.608][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.609][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:30.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.612][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.613][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.613][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:30.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:30.615][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.616][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:03:30.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:30.618][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.619][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.620][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:30.620][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:30.620][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:30.620][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:30.620][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:30.621][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:30.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.624][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:30.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.627][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.628][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.629][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:30.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:30.630][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.631][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.632][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:03:30.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.635][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:30.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:30.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.642][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:30.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:30.644][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.644][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:03:30.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:30.646][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.648][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:03:30.648][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:03:30.648][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:03:30.648][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:03:30.648][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:03:30.649][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:30.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:30.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.656][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:30.657][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:30.658][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.659][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.660][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:03:30.662][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.663][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:03:30.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:30.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.668][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.669][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.670][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:03:30.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:30.672][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.673][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:03:30.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:30.674][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.676][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:30.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:30.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.684][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:30.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:30.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.687][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.688][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:03:30.690][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.691][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:03:30.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:30.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.698][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:03:30.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:30.700][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.700][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:03:30.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:30.702][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:30.704][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:03:30.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:30.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:30.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:30.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:30.712][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:30.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:30.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:30.715][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:30.720][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:30.721][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.792][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:03:30.793][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:03:30.794][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:03:30.796][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:03:30.797][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:03:30.799][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:03:30.800][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:30.801][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:30.803][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:03:30.804][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:03:30.805][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:03:30.807][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:03:30.808][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:03:30.809][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:03:30.811][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:03:30.812][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:03:30.814][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:03:30.815][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:03:30.816][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:03:30.818][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:03:30.819][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:03:30.820][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:03:30.822][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:03:30.823][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:03:30.824][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:03:30.826][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:03:30.827][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:03:30.832][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:03:30.834][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:03:30.835][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:03:30.836][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:03:30.838][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:03:30.839][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:03:30.840][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:03:30.842][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:03:30.843][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:03:30.844][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:03:30.846][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:03:30.847][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:03:30.848][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:03:30.850][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:03:30.851][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:03:30.852][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:03:30.854][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:03:30.855][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:03:30.856][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:03:30.858][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:03:30.859][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:03:30.860][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:03:30.861][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:03:30.863][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:03:30.864][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:03:30.865][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:03:30.867][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:03:30.868][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:03:30.869][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:03:30.871][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:03:30.872][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:03:30.873][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:03:30.874][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:03:30.876][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:03:30.877][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:03:30.878][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:03:30.880][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:03:30.881][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:03:30.882][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:03:30.884][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:03:30.885][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:03:30.886][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:03:30.887][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:03:30.889][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:03:30.890][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:03:30.891][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:03:30.893][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:03:30.894][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:03:30.895][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:03:30.897][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:03:30.898][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:03:30.899][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:03:30.901][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:03:30.902][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:03:30.903][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:03:30.904][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:03:30.906][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:03:30.907][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-04 16:03:30.908][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:03:30.909][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.911][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:30.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:30.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:30.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:30.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:30.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:30.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:30.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:31.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:31.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:31.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:31.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:31.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:31.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:31.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:31.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:03:31.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:31.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:31.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:31.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:31.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:03:31.012][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-04 16:03:31.014][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:31.015][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:31.016][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-04 16:03:31.017][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:31.018][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:03:31.019][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:31.020][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-04 16:03:31.021][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:31.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:03:31.023][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-04 16:03:31.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:03:31.025][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:31.026][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-04 16:03:31.027][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-04 16:03:31.028][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-04 16:03:31.029][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:03:31.030][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:31.031][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:03:31.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:31.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:31.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:03:31.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:03:31.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:03:31.036][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:03:31.037][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:31.037][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-04 16:03:31.037][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-04 16:03:31.037][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-04 16:03:31.038][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:03:31.039][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:03:31.040][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:03:31.041][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:03:31.042][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-04 16:03:31.045][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-04 16:03:31.052][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-04 16:03:31.053][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:03:31.054][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-04 16:03:31.055][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:03:31.056][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:03:31.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:03:31.057][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:03:31.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:03:31.059][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:03:31.060][FUN] Functions in observer 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 0 | PASS 85 ]

══ 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 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* 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 ‘1.12.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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:
  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 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)