Back to Long Tests report for BioC 3.22

This page was generated on 2025-07-12 23:55 -0400 (Sat, 12 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4783
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4520
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4564
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/29HostnameOS / ArchCHECK
biodbNci 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-07-12 09:55 -0400 (Sat, 12 Jul 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 536802f
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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: 1.13.0
Command: /home/biocbuild/bbs-3.22-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_1.13.0.tar.gz
StartedAt: 2025-07-12 16:02:32 -0400 (Sat, 12 Jul 2025)
EndedAt: 2025-07-12 16:03:30 -0400 (Sat, 12 Jul 2025)
EllapsedTime: 57.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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Copyright (C) 2025 The R Foundation for Statistical Computing
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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 [2025-07-12 16:03:26.540][biodb::testContext]
biodb.INFO [2025-07-12 16:03:26.542][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:03:26.543][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-07-12 16:03:26.543][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:03:26.544][biodb::testContext]
biodb.INFO [2025-07-12 16:03:26.550][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:03:26.552][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-07-12 16:03:26.558][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:26.559][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-12 16:03:26.560][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.563][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-12 16:03:26.580][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.582][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[2025-07-12 16:03:26.583][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-12 16:03:26.584][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.587][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-12 16:03:26.588][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-12 16:03:26.589][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-12 16:03:26.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.592][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-12 16:03:26.593][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-12 16:03:26.594][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.598][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-12 16:03:26.598][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-12 16:03:26.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.602][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-12 16:03:26.603][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-12 16:03:26.604][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-12 16:03:26.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.607][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-12 16:03:26.608][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.611][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-12 16:03:26.612][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-12 16:03:26.613][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-12 16:03:26.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.616][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:03:26.617][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-12 16:03:26.618][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-12 16:03:26.619][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-12 16:03:26.620][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-12 16:03:26.621][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-12 16:03:26.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.624][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-12 16:03:26.625][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-12 16:03:26.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.628][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-12 16:03:26.629][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-12 16:03:26.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.632][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-12 16:03:26.633][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-12 16:03:26.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.637][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-12 16:03:26.637][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-12 16:03:26.638][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-12 16:03:26.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.642][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:03:26.643][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-12 16:03:26.647][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-12 16:03:26.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.650][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-12 16:03:26.651][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-12 16:03:26.652][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-12 16:03:26.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.657][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-12 16:03:26.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.707][self$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[2025-07-12 16:03:26.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:26.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.712][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.713][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:03:26.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:26.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.716][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-12 16:03:26.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:26.718][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.719][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.720][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:03:26.720][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:03:26.720][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:03:26.720][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:03:26.720][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:03:26.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:26.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.723][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:26.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.726][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.727][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:26.728][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:26.729][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.730][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.731][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-12 16:03:26.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.734][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:03:26.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.735][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:26.736][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.739][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:03:26.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:26.742][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.743][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-12 16:03:26.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:26.744][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.745][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.746][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:03:26.746][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:03:26.746][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:03:26.746][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:03:26.746][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:03:26.747][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:26.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.750][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:26.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.752][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.753][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.754][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:26.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:26.756][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.757][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.758][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-12 16:03:26.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.760][self$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[2025-07-12 16:03:26.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:26.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.764][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.765][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.766][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:03:26.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:26.768][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.769][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-12 16:03:26.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:26.771][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.772][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.773][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.774][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:26.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:26.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.780][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:26.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:26.782][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.783][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.784][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-12 16:03:26.786][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.787][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:03:26.788][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.788][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:26.789][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.790][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.792][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.793][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:03:26.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:26.795][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.796][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-12 16:03:26.797][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:26.798][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.798][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:26.799][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.800][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:26.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.803][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:26.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:26.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:26.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:26.806][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:26.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:26.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:26.810][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:26.813][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:26.814][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:26.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:26.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:26.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:26.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:26.884][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-12 16:03:26.888][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-12 16:03:26.890][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-12 16:03:26.891][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-12 16:03:26.892][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-12 16:03:26.894][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-12 16:03:26.895][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-12 16:03:26.896][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-12 16:03:26.897][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-12 16:03:26.899][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-12 16:03:26.900][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-12 16:03:26.901][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-12 16:03:26.903][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-12 16:03:26.904][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-12 16:03:26.905][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-12 16:03:26.906][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-12 16:03:26.908][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-12 16:03:26.909][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-12 16:03:26.910][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-12 16:03:26.911][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-12 16:03:26.913][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-12 16:03:26.914][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-12 16:03:26.915][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-12 16:03:26.916][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-12 16:03:26.918][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-12 16:03:26.919][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-12 16:03:26.920][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-12 16:03:26.922][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-12 16:03:26.923][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-12 16:03:26.924][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-12 16:03:26.925][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-12 16:03:26.927][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-12 16:03:26.928][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-12 16:03:26.929][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-12 16:03:26.930][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-12 16:03:26.932][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-12 16:03:26.933][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-12 16:03:26.934][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-12 16:03:26.935][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-12 16:03:26.937][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-12 16:03:26.938][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-12 16:03:26.939][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-12 16:03:26.940][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-12 16:03:26.942][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-12 16:03:26.943][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-12 16:03:26.944][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-12 16:03:26.946][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-12 16:03:26.947][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-12 16:03:26.948][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-12 16:03:26.949][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-12 16:03:26.951][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-12 16:03:26.952][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-12 16:03:26.953][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-12 16:03:26.954][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-12 16:03:26.956][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-12 16:03:26.957][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-12 16:03:26.958][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-12 16:03:26.960][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-12 16:03:26.961][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-12 16:03:26.962][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-12 16:03:26.963][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-12 16:03:26.965][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-12 16:03:26.966][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-12 16:03:26.967][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-12 16:03:26.968][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-12 16:03:26.970][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-12 16:03:26.971][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-12 16:03:26.972][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-12 16:03:26.973][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-12 16:03:26.975][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-12 16:03:26.976][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-12 16:03:26.977][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-12 16:03:26.979][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-12 16:03:26.980][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-12 16:03:26.981][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-12 16:03:26.986][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-12 16:03:26.988][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-12 16:03:26.989][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-12 16:03:26.990][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-12 16:03:26.991][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-12 16:03:26.993][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-12 16:03:26.994][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-12 16:03:26.995][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-12 16:03:27.001][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-12 16:03:27.002][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:03:27.005][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:27.006][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.007][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.008][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[2025-07-12 16:03:27.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:27.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:27.104][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-07-12 16:03:27.113][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-07-12 16:03:27.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:27.116][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-07-12 16:03:27.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:27.117][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:27.118][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:27.119][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-07-12 16:03:27.120][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:27.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:27.122][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-07-12 16:03:27.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:27.124][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:27.125][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-07-12 16:03:27.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-07-12 16:03:27.127][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-07-12 16:03:27.128][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:27.128][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:27.129][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-12 16:03:27.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:27.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:27.132][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:27.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:27.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:27.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:27.135][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-07-12 16:03:27.135][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-07-12 16:03:27.135][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-07-12 16:03:27.135][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-07-12 16:03:27.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:27.137][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:27.138][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:27.139][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:27.148][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-07-12 16:03:27.167][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-07-12 16:03:27.191][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-07-12 16:03:27.201][biodb::testThat]
biodb.INFO [2025-07-12 16:03:27.202][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-07-12 16:03:27.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:27.204][biodb::testThat]
biodb.TRACE[2025-07-12 16:03:27.208][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-07-12 16:03:27.210][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-07-12 16:03:27.213][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-07-12 16:03:27.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-12 16:03:27.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-12 16:03:27.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.308][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.339][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.357][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.365][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-12 16:03:27.421][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-07-12 16:03:27.423][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.427][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.430][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-12 16:03:27.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-12 16:03:27.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.434][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-12 16:03:27.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-12 16:03:27.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.453][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.487][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.490][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.494][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.514][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.516][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.538][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.541][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.562][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.563][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.564][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.586][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.587][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.588][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.613][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.614][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.616][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.627][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.629][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.633][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.634][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.636][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.639][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.642][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.648][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.652][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.653][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.654][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.670][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-07-12 16:03:27.702][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-07-12 16:03:27.703][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-07-12 16:03:27.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-07-12 16:03:27.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:27.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:27.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:27.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:27.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:27.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-07-12 16:03:27.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.778][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.782][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:27.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:27.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.786][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:27.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:27.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:27.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:27.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:27.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:27.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:27.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:27.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.842][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.846][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.853][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-07-12 16:03:27.881][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-07-12 16:03:27.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-07-12 16:03:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-07-12 16:03:27.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-07-12 16:03:27.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-07-12 16:03:27.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-07-12 16:03:27.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.922][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.955][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.959][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-07-12 16:03:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.987][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.990][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:27.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:27.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:27.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.007][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.011][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.015][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.016][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.017][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.018][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.041][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.062][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.063][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.065][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.086][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.087][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.089][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.114][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.115][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.145][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.146][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.148][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.161][ef$get] Asked field names are: accession.
biodb.TRACE[2025-07-12 16:03:28.162][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-07-12 16:03:28.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.164][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.168][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.169][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-07-12 16:03:28.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.171][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.175][ef$get] Asked field names are: formula.
biodb.TRACE[2025-07-12 16:03:28.176][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-07-12 16:03:28.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.178][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-07-12 16:03:28.187][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-07-12 16:03:28.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.190][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.197][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.198][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-07-12 16:03:28.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.201][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.208][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-07-12 16:03:28.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.212][ef$get] fields variable is a list.
biodb.TRACE[2025-07-12 16:03:28.218][ef$get] Asked field names are: name.
biodb.TRACE[2025-07-12 16:03:28.220][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-07-12 16:03:28.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-07-12 16:03:28.223][ef$get] fields variable is a list.
biodb.INFO [2025-07-12 16:03:28.233][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.235][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-07-12 16:03:28.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.238][biodb::testThat]
biodb.DEBUG[2025-07-12 16:03:28.241][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-07-12 16:03:28.244][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-07-12 16:03:28.248][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-07-12 16:03:28.296][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-07-12 16:03:28.298][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-07-12 16:03:28.299][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-07-12 16:03:28.341][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.342][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-07-12 16:03:28.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.344][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.349][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.350][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-07-12 16:03:28.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.352][biodb::testThat]
biodb.WARN [2025-07-12 16:03:28.369][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-07-12 16:03:28.387][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-07-12 16:03:28.394][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.395][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-07-12 16:03:28.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.397][biodb::testThat]
biodb.DEBUG[2025-07-12 16:03:28.412][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-07-12 16:03:28.460][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-07-12 16:03:28.462][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-07-12 16:03:28.463][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-07-12 16:03:28.464][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-07-12 16:03:28.476][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-07-12 16:03:28.498][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.499][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-07-12 16:03:28.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.500][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.506][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.507][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-07-12 16:03:28.508][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.509][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.515][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.516][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-07-12 16:03:28.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.518][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.523][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.524][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-07-12 16:03:28.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-07-12 16:03:28.525][biodb::testThat]
biodb.INFO [2025-07-12 16:03:28.530][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-07-12 16:03:28.531][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-07-12 16:03:28.532][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-12 16:03:28.537][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.538][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.540][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-07-12 16:03:28.549][biodb::testContext]
biodb.INFO [2025-07-12 16:03:28.550][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:03:28.551][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-07-12 16:03:28.552][biodb::testContext] ********************************************************************************
biodb.INFO [2025-07-12 16:03:28.553][biodb::testContext]
biodb.INFO [2025-07-12 16:03:28.554][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:03:28.556][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-07-12 16:03:28.559][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:28.560][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-07-12 16:03:28.561][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.565][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-07-12 16:03:28.566][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.569][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-07-12 16:03:28.570][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.573][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-07-12 16:03:28.574][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-07-12 16:03:28.575][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-07-12 16:03:28.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.578][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-07-12 16:03:28.579][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-07-12 16:03:28.580][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.583][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-07-12 16:03:28.584][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-07-12 16:03:28.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.588][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-07-12 16:03:28.589][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-07-12 16:03:28.589][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-07-12 16:03:28.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.593][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-07-12 16:03:28.594][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.597][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-07-12 16:03:28.598][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-07-12 16:03:28.599][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-07-12 16:03:28.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.602][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:03:28.603][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-07-12 16:03:28.604][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-07-12 16:03:28.605][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-07-12 16:03:28.606][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-07-12 16:03:28.607][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-07-12 16:03:28.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.610][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-07-12 16:03:28.611][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-07-12 16:03:28.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.614][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-07-12 16:03:28.615][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-07-12 16:03:28.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.618][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-07-12 16:03:28.619][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-07-12 16:03:28.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.623][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-07-12 16:03:28.624][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-07-12 16:03:28.625][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-07-12 16:03:28.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.628][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-07-12 16:03:28.629][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-07-12 16:03:28.633][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-07-12 16:03:28.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.636][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-07-12 16:03:28.637][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-07-12 16:03:28.638][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-07-12 16:03:28.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.642][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-07-12 16:03:28.643][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.644][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-07-12 16:03:28.645][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.646][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:28.647][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.649][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.650][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.651][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:03:28.651][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:28.652][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.653][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-07-12 16:03:28.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:28.655][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:03:28.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:03:28.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:03:28.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:03:28.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:03:28.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:28.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:28.665][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.666][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.667][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.668][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:28.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:28.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.672][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.673][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-07-12 16:03:28.674][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.675][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:03:28.676][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:28.678][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.682][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:03:28.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:28.683][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.684][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-07-12 16:03:28.685][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:28.686][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.687][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.688][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-07-12 16:03:28.688][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-07-12 16:03:28.688][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-07-12 16:03:28.688][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-07-12 16:03:28.688][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-07-12 16:03:28.689][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:28.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:28.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.695][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.696][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:28.697][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:28.697][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.698][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.699][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-07-12 16:03:28.701][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.702][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-07-12 16:03:28.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:28.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.706][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.708][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-07-12 16:03:28.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:28.710][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.711][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-07-12 16:03:28.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:28.713][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.715][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.715][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:28.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:28.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.720][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.721][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.722][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:28.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:28.724][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.725][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.726][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-07-12 16:03:28.727][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.728][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-07-12 16:03:28.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:28.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.735][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-07-12 16:03:28.736][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:28.736][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.737][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-07-12 16:03:28.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:28.739][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:28.741][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-07-12 16:03:28.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.744][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:28.745][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:28.746][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:28.747][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:28.748][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.749][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:28.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:28.750][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:28.751][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:28.752][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:28.753][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.774][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[2025-07-12 16:03:28.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:28.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.823][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-07-12 16:03:28.825][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-07-12 16:03:28.826][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-07-12 16:03:28.827][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-07-12 16:03:28.829][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-07-12 16:03:28.830][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-07-12 16:03:28.831][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-07-12 16:03:28.832][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-07-12 16:03:28.834][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-07-12 16:03:28.835][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-07-12 16:03:28.836][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-07-12 16:03:28.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-07-12 16:03:28.839][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-07-12 16:03:28.840][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-07-12 16:03:28.841][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-07-12 16:03:28.842][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-07-12 16:03:28.844][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-07-12 16:03:28.845][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-07-12 16:03:28.846][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-07-12 16:03:28.848][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-07-12 16:03:28.849][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-07-12 16:03:28.850][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-07-12 16:03:28.851][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-07-12 16:03:28.853][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-07-12 16:03:28.854][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-07-12 16:03:28.855][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-07-12 16:03:28.856][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-07-12 16:03:28.858][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-07-12 16:03:28.859][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-07-12 16:03:28.860][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-07-12 16:03:28.862][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-07-12 16:03:28.863][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-07-12 16:03:28.864][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-07-12 16:03:28.865][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-07-12 16:03:28.867][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-07-12 16:03:28.868][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-07-12 16:03:28.869][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-07-12 16:03:28.870][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-07-12 16:03:28.872][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-07-12 16:03:28.873][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-07-12 16:03:28.874][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-07-12 16:03:28.876][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-07-12 16:03:28.877][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-07-12 16:03:28.878][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-07-12 16:03:28.879][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-07-12 16:03:28.881][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-07-12 16:03:28.882][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-07-12 16:03:28.883][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-07-12 16:03:28.885][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-07-12 16:03:28.886][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-07-12 16:03:28.887][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-07-12 16:03:28.888][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-07-12 16:03:28.890][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-07-12 16:03:28.891][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-07-12 16:03:28.892][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-07-12 16:03:28.893][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-07-12 16:03:28.895][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-07-12 16:03:28.896][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-07-12 16:03:28.901][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-07-12 16:03:28.903][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-07-12 16:03:28.904][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-07-12 16:03:28.905][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-07-12 16:03:28.906][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-07-12 16:03:28.908][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-07-12 16:03:28.909][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-07-12 16:03:28.910][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-07-12 16:03:28.911][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-07-12 16:03:28.913][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-07-12 16:03:28.914][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-07-12 16:03:28.915][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-07-12 16:03:28.916][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-07-12 16:03:28.918][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-07-12 16:03:28.919][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-07-12 16:03:28.920][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-07-12 16:03:28.922][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-07-12 16:03:28.923][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-07-12 16:03:28.924][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-07-12 16:03:28.925][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-07-12 16:03:28.927][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-07-12 16:03:28.928][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-07-12 16:03:28.929][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-07-12 16:03:28.930][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-07-12 16:03:28.932][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-07-12 16:03:28.933][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-07-12 16:03:28.935][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-07-12 16:03:28.935][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-07-12 16:03:28.936][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.938][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:28.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:28.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:28.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:28.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:28.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:28.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:28.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 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[2025-07-12 16:03:29.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:29.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:29.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:29.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:29.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:29.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:29.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:29.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:29.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-07-12 16:03:29.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-07-12 16:03:29.035][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-07-12 16:03:29.036][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-07-12 16:03:29.038][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:29.038][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-07-12 16:03:29.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:29.040][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-07-12 16:03:29.041][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:29.042][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-07-12 16:03:29.043][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:29.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-07-12 16:03:29.045][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-07-12 16:03:29.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-07-12 16:03:29.047][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:29.048][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-07-12 16:03:29.048][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-07-12 16:03:29.049][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-07-12 16:03:29.050][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-07-12 16:03:29.051][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:29.052][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-07-12 16:03:29.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:29.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:29.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-07-12 16:03:29.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-07-12 16:03:29.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-07-12 16:03:29.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-07-12 16:03:29.058][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-07-12 16:03:29.058][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-07-12 16:03:29.058][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-07-12 16:03:29.058][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-07-12 16:03:29.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-07-12 16:03:29.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-07-12 16:03:29.061][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-07-12 16:03:29.062][self$setPropertyValue]
biodb.DEBUG[2025-07-12 16:03:29.063][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-07-12 16:03:29.066][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-07-12 16:03:29.069][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-07-12 16:03:29.070][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-07-12 16:03:29.071][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-07-12 16:03:29.072][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-07-12 16:03:29.073][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-07-12 16:03:29.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-07-12 16:03:29.075][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-07-12 16:03:29.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-07-12 16:03:29.076][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-07-12 16:03:29.077][FUN] Functions in observer 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-3.22-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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 24.04.2 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 ‘1.13.0’
* 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 ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.0’
** 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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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)