Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-14 23:55 -0500 (Sat, 14 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4889
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4679
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-02-14 09:55 -0500 (Sat, 14 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-02-14 16:01:16 -0500 (Sat, 14 Feb 2026)
EndedAt: 2026-02-14 16:02:40 -0500 (Sat, 14 Feb 2026)
EllapsedTime: 83.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-02-14 16:02:34.594][biodb::testContext]
biodb.INFO [2026-02-14 16:02:34.600][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:34.601][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-14 16:02:34.603][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:34.604][biodb::testContext]
biodb.INFO [2026-02-14 16:02:34.616][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:34.619][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:34.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:34.629][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-14 16:02:34.639][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.646][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-14 16:02:34.669][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.683][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-14 16:02:34.685][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.692][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-14 16:02:34.694][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-14 16:02:34.696][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-14 16:02:34.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.701][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-14 16:02:34.702][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-14 16:02:34.704][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.709][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-14 16:02:34.710][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-14 16:02:34.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.716][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-14 16:02:34.717][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-14 16:02:34.718][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-14 16:02:34.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.726][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-14 16:02:34.734][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.740][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-14 16:02:34.741][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-14 16:02:34.743][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-14 16:02:34.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.750][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:34.752][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-14 16:02:34.754][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-14 16:02:34.755][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-14 16:02:34.756][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-14 16:02:34.757][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-14 16:02:34.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.762][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-14 16:02:34.763][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-14 16:02:34.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.769][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-14 16:02:34.772][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-14 16:02:34.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.778][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-14 16:02:34.779][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-14 16:02:34.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.786][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-14 16:02:34.788][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-14 16:02:34.789][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-14 16:02:34.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.797][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:34.799][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-14 16:02:34.810][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-14 16:02:34.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.817][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-14 16:02:34.819][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-14 16:02:34.820][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-14 16:02:34.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:34.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:34.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:34.835][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-14 16:02:34.886][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:34.914][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-14 16:02:34.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:34.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:34.923][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:34.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:34.925][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:34.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:34.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.936][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-14 16:02:34.937][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:34.938][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:34.939][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.941][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:34.941][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:34.941][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:34.941][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:34.941][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:34.947][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:34.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:34.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:34.951][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:34.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:34.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:34.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:34.957][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:34.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:34.960][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:34.961][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:34.962][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:34.964][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-14 16:02:34.966][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:34.967][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:34.969][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:34.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:34.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:34.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:34.980][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:34.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:34.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.984][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-14 16:02:34.985][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:34.987][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:34.988][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:34.989][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:34.989][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:34.989][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:34.989][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:34.989][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:34.991][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:34.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:34.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:34.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:34.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:34.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:34.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.000][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.002][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:35.003][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:35.005][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.006][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.007][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-14 16:02:35.010][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.011][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-14 16:02:35.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:35.017][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.021][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.026][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:35.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:35.029][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.031][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-14 16:02:35.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:35.037][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.040][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.041][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:35.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:35.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.051][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.053][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.054][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:35.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:35.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.058][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.060][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-14 16:02:35.064][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.066][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:35.068][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.071][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:35.073][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.075][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.076][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.077][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.078][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:35.080][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:35.081][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.082][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-14 16:02:35.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:35.085][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.086][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.087][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.089][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:35.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:35.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.100][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:35.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:35.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.109][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.113][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:35.114][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.250][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-14 16:02:35.255][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-14 16:02:35.257][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-14 16:02:35.259][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-14 16:02:35.261][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-14 16:02:35.262][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:02:35.264][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:35.292][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:35.294][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-14 16:02:35.295][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:02:35.299][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:02:35.302][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-14 16:02:35.305][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:35.309][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:35.313][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-14 16:02:35.316][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:02:35.319][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-14 16:02:35.320][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-14 16:02:35.322][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-14 16:02:35.324][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-14 16:02:35.326][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-14 16:02:35.328][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-14 16:02:35.330][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-14 16:02:35.332][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-14 16:02:35.334][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-14 16:02:35.335][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-14 16:02:35.337][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-14 16:02:35.339][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-14 16:02:35.341][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-14 16:02:35.342][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-14 16:02:35.344][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-14 16:02:35.346][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-14 16:02:35.348][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-14 16:02:35.350][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-14 16:02:35.352][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-14 16:02:35.354][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-14 16:02:35.355][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-14 16:02:35.357][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-14 16:02:35.379][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-14 16:02:35.381][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-14 16:02:35.383][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-14 16:02:35.385][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-14 16:02:35.387][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-14 16:02:35.390][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-14 16:02:35.392][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-14 16:02:35.395][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-14 16:02:35.397][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-14 16:02:35.400][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-14 16:02:35.404][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-14 16:02:35.408][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-14 16:02:35.410][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-14 16:02:35.412][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-14 16:02:35.414][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-14 16:02:35.416][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-14 16:02:35.418][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-14 16:02:35.421][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-14 16:02:35.423][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-14 16:02:35.425][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-14 16:02:35.427][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-14 16:02:35.428][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-14 16:02:35.430][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-14 16:02:35.432][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-14 16:02:35.434][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-14 16:02:35.436][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-14 16:02:35.437][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-14 16:02:35.439][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-14 16:02:35.441][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-14 16:02:35.466][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-14 16:02:35.469][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-14 16:02:35.472][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-14 16:02:35.475][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-14 16:02:35.478][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-14 16:02:35.481][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-14 16:02:35.483][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-14 16:02:35.485][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-14 16:02:35.488][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-14 16:02:35.491][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-14 16:02:35.494][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-14 16:02:35.496][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-14 16:02:35.498][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-14 16:02:35.500][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-14 16:02:35.502][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-14 16:02:35.505][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-14 16:02:35.514][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-14 16:02:35.517][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:35.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:35.554][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.557][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.587][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[2026-02-14 16:02:35.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:35.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:35.753][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:35.769][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-14 16:02:35.772][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.773][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-14 16:02:35.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.776][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:35.777][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.778][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-14 16:02:35.779][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.782][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-14 16:02:35.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:35.785][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.786][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-14 16:02:35.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-14 16:02:35.789][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-14 16:02:35.790][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:35.792][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.796][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-14 16:02:35.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:35.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:35.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:35.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:35.810][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:02:35.810][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:02:35.810][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-14 16:02:35.810][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-14 16:02:35.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:35.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:35.815][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:35.816][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:35.824][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-14 16:02:35.846][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-14 16:02:35.862][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-14 16:02:35.871][biodb::testThat]
biodb.INFO [2026-02-14 16:02:35.873][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-14 16:02:35.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:35.876][biodb::testThat]
biodb.TRACE[2026-02-14 16:02:35.883][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-02-14 16:02:35.885][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-14 16:02:35.892][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-14 16:02:35.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-14 16:02:35.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:35.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:35.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:35.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:35.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:35.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-14 16:02:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:35.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:35.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:35.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:35.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:35.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:35.982][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:35.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:35.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:35.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.079][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.101][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:02:36.200][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-02-14 16:02:36.203][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:36.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:36.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.219][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:36.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:36.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:36.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.307][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.389][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.401][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:36.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.450][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.453][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.454][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.456][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.491][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.492][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.494][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.495][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.554][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.555][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.557][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.559][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.590][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.619][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.622][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.666][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.667][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.668][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.670][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.692][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.696][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.697][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.699][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.717][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.718][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.720][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.721][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.730][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:36.731][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:36.733][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.734][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.741][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.743][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:36.744][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.745][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.752][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.754][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.755][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.757][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.785][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-02-14 16:02:36.837][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-14 16:02:36.838][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-14 16:02:36.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-14 16:02:36.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:36.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:36.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:36.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:36.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:36.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-14 16:02:36.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:36.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.918][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:36.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:36.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.969][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.976][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:36.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:36.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:36.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:36.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:36.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.084][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.091][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.103][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-14 16:02:37.173][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-02-14 16:02:37.202][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-14 16:02:37.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-14 16:02:37.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:37.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-14 16:02:37.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:37.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-14 16:02:37.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.335][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.420][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.426][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.433][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-14 16:02:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.510][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.513][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.515][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.536][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.543][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.548][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.553][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.554][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.555][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.557][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.558][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.614][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.617][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.618][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.620][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.644][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.654][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.657][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.658][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.659][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.671][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.717][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.718][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.719][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.720][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.769][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.770][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.772][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.809][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.810][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.811][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.813][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.836][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-14 16:02:37.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-14 16:02:37.845][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.846][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.871][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.874][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-14 16:02:37.876][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.878][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.891][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-14 16:02:37.893][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-14 16:02:37.894][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.895][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.904][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-14 16:02:37.906][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-14 16:02:37.907][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.908][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.924][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-14 16:02:37.925][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.926][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.940][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.941][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-14 16:02:37.943][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.944][ef$get] fields variable is a list.
biodb.TRACE[2026-02-14 16:02:37.972][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-14 16:02:37.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-14 16:02:37.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-14 16:02:37.977][ef$get] fields variable is a list.
biodb.INFO [2026-02-14 16:02:37.993][biodb::testThat]
biodb.INFO [2026-02-14 16:02:37.994][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-14 16:02:37.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:37.997][biodb::testThat]
biodb.DEBUG[2026-02-14 16:02:38.000][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-02-14 16:02:38.005][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-02-14 16:02:38.009][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:38.054][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-14 16:02:38.056][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-14 16:02:38.057][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-14 16:02:38.295][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.296][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-14 16:02:38.298][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.299][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.335][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.337][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-14 16:02:38.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.341][biodb::testThat]
biodb.WARN [2026-02-14 16:02:38.376][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-14 16:02:38.401][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-14 16:02:38.420][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.421][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-14 16:02:38.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.424][biodb::testThat]
biodb.DEBUG[2026-02-14 16:02:38.448][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-02-14 16:02:38.512][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-14 16:02:38.514][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-14 16:02:38.516][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-14 16:02:38.518][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-14 16:02:38.541][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-14 16:02:38.660][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.662][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-14 16:02:38.667][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.669][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.686][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.688][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-14 16:02:38.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.691][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.704][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.706][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-14 16:02:38.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.708][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.720][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.722][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-14 16:02:38.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-14 16:02:38.724][biodb::testThat]
biodb.INFO [2026-02-14 16:02:38.735][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-14 16:02:38.736][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-14 16:02:38.738][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-14 16:02:38.742][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:38.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:38.750][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:38.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:38.753][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-14 16:02:38.767][biodb::testContext]
biodb.INFO [2026-02-14 16:02:38.769][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:38.770][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-02-14 16:02:38.771][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-14 16:02:38.772][biodb::testContext]
biodb.INFO [2026-02-14 16:02:38.775][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:38.777][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:38.781][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:38.783][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-14 16:02:38.784][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.790][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-14 16:02:38.791][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.796][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-14 16:02:38.797][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.802][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-14 16:02:38.803][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-14 16:02:38.805][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-14 16:02:38.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.810][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-14 16:02:38.812][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-14 16:02:38.817][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.825][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-14 16:02:38.833][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-14 16:02:38.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.838][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-14 16:02:38.839][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-14 16:02:38.840][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-14 16:02:38.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.845][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-14 16:02:38.847][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.852][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-14 16:02:38.853][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-14 16:02:38.854][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-14 16:02:38.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.861][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:38.863][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-14 16:02:38.864][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-14 16:02:38.866][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-14 16:02:38.867][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-14 16:02:38.868][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-14 16:02:38.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.875][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-14 16:02:38.876][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-14 16:02:38.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.881][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-14 16:02:38.882][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-14 16:02:38.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.887][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-14 16:02:38.889][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-14 16:02:38.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.894][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-14 16:02:38.895][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-14 16:02:38.897][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-14 16:02:38.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.904][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-14 16:02:38.905][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-14 16:02:38.919][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-14 16:02:38.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.927][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-14 16:02:38.928][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-14 16:02:38.929][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-14 16:02:38.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:38.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:38.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:38.934][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-14 16:02:38.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:38.938][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-14 16:02:38.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:38.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:38.946][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:38.947][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:38.949][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:38.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:38.952][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.954][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-14 16:02:38.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:38.957][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:38.959][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.961][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:38.961][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:38.961][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:38.961][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:38.961][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:38.963][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:38.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:38.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:38.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:38.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:38.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:38.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:38.972][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:38.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:38.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:38.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:38.977][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:38.979][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-14 16:02:38.981][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:38.983][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:38.984][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:38.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:38.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:38.992][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:38.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:38.995][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:39.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:39.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.005][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-14 16:02:39.006][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:39.007][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.010][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-14 16:02:39.010][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-14 16:02:39.010][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-14 16:02:39.010][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-14 16:02:39.010][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-14 16:02:39.011][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:39.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:39.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.024][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:39.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:39.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.028][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.030][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-14 16:02:39.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.033][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-14 16:02:39.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:39.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.038][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.040][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.041][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.044][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-14 16:02:39.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:39.048][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.051][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-14 16:02:39.053][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:39.055][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.057][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.058][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.059][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:39.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:39.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.068][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:39.070][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:39.071][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.073][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.078][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-14 16:02:39.080][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.082][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-14 16:02:39.083][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.084][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:39.085][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.087][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.088][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.094][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-14 16:02:39.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:39.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.098][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-14 16:02:39.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:39.105][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.108][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-14 16:02:39.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:39.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.122][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.123][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:39.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:39.127][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.128][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:39.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.243][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-14 16:02:39.245][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-14 16:02:39.246][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-14 16:02:39.248][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-14 16:02:39.250][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-14 16:02:39.251][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-14 16:02:39.253][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:39.255][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:39.257][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-14 16:02:39.259][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-14 16:02:39.261][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-14 16:02:39.263][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-14 16:02:39.265][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-14 16:02:39.267][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-14 16:02:39.272][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-14 16:02:39.273][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-14 16:02:39.275][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-14 16:02:39.280][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-14 16:02:39.282][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-14 16:02:39.287][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-14 16:02:39.288][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-14 16:02:39.290][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-14 16:02:39.292][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-14 16:02:39.298][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-14 16:02:39.300][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-14 16:02:39.301][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-14 16:02:39.303][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-14 16:02:39.305][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-14 16:02:39.306][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-14 16:02:39.308][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-14 16:02:39.310][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-14 16:02:39.311][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-14 16:02:39.313][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-14 16:02:39.319][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-14 16:02:39.321][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-14 16:02:39.323][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-14 16:02:39.324][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-14 16:02:39.326][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-14 16:02:39.328][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-14 16:02:39.329][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-14 16:02:39.331][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-14 16:02:39.333][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-14 16:02:39.335][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-14 16:02:39.337][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-14 16:02:39.339][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-14 16:02:39.341][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-14 16:02:39.343][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-14 16:02:39.345][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-14 16:02:39.347][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-14 16:02:39.348][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-14 16:02:39.350][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-14 16:02:39.353][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-14 16:02:39.354][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-14 16:02:39.356][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-14 16:02:39.358][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-14 16:02:39.360][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-14 16:02:39.362][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-14 16:02:39.366][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-14 16:02:39.368][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-14 16:02:39.370][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-14 16:02:39.376][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-14 16:02:39.377][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-14 16:02:39.381][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-14 16:02:39.383][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-14 16:02:39.384][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-14 16:02:39.386][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-14 16:02:39.388][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-14 16:02:39.390][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-14 16:02:39.391][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-14 16:02:39.393][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-14 16:02:39.395][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-14 16:02:39.400][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-14 16:02:39.402][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-14 16:02:39.404][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-14 16:02:39.406][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-14 16:02:39.408][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-14 16:02:39.410][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-14 16:02:39.412][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-14 16:02:39.414][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-14 16:02:39.415][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-14 16:02:39.417][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-14 16:02:39.419][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-14 16:02:39.421][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-14 16:02:39.423][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-14 16:02:39.425][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-14 16:02:39.426][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-14 16:02:39.428][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.430][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-14 16:02:39.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.596][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[2026-02-14 16:02:39.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-14 16:02:39.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.606][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[2026-02-14 16:02:39.609][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-14 16:02:39.611][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-14 16:02:39.616][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.618][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-14 16:02:39.620][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-14 16:02:39.625][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.627][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-14 16:02:39.629][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.630][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.632][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-14 16:02:39.634][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-14 16:02:39.636][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.637][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-14 16:02:39.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-14 16:02:39.640][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-14 16:02:39.641][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-14 16:02:39.642][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.644][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-14 16:02:39.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-14 16:02:39.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-14 16:02:39.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-14 16:02:39.651][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-14 16:02:39.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:02:39.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-14 16:02:39.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-14 16:02:39.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-14 16:02:39.653][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-14 16:02:39.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-14 16:02:39.656][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-14 16:02:39.657][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-14 16:02:39.659][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-14 16:02:39.663][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-14 16:02:39.674][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-14 16:02:39.681][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-14 16:02:39.683][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-14 16:02:39.684][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-14 16:02:39.685][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-14 16:02:39.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-14 16:02:39.687][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-14 16:02:39.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-14 16:02:39.690][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-14 16:02:39.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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