Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-07 23:55 -0500 (Sat, 07 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4888
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4678
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: 2026-02-07 09:55 -0500 (Sat, 07 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: 2026-02-07 16:01:18 -0500 (Sat, 07 Feb 2026)
EndedAt: 2026-02-07 16:02:45 -0500 (Sat, 07 Feb 2026)
EllapsedTime: 87.7 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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Type 'license()' or 'licence()' for distribution details.

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
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 [2026-02-07 16:02:40.742][biodb::testContext]
biodb.INFO [2026-02-07 16:02:40.745][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:40.747][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-07 16:02:40.748][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:40.749][biodb::testContext]
biodb.INFO [2026-02-07 16:02:40.755][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:40.757][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:40.764][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:40.766][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:40.767][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.772][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:40.796][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.800][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:40.802][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.806][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:40.807][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:40.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:40.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.813][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:40.814][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:40.816][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.820][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:40.822][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:40.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.826][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:40.827][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:40.829][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:40.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.833][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:40.835][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.839][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:40.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:40.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:40.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.847][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:40.848][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:40.849][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:40.850][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:40.852][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:40.853][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:40.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.858][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:40.859][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:40.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.864][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:40.865][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:40.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.869][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:40.871][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:40.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.875][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:40.877][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:40.878][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:40.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.883][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:40.884][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:40.895][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:40.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.899][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:40.901][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:40.902][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:40.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:40.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:40.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:40.909][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:40.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:40.981][self$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[2026-02-07 16:02:40.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:40.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:40.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:40.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:40.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:40.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:40.990][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:40.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:40.993][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:40.994][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:40.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:40.996][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:40.998][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:40.999][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:40.999][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:40.999][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:40.999][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:40.999][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:41.000][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:41.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.004][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:41.005][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.007][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.009][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:41.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:41.012][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.013][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.015][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:41.017][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.018][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:41.020][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.021][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:41.022][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.023][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.027][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:41.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:41.030][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.031][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:41.032][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:41.033][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.036][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:41.036][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:41.036][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:41.036][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:41.036][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:41.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:41.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.041][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:41.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.046][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.047][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:41.048][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:41.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.050][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.052][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:41.054][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.055][self$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[2026-02-07 16:02:41.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:41.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.064][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:41.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:41.067][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.068][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:41.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:41.070][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.072][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.073][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.074][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:41.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:41.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.083][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.084][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:41.085][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:41.086][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.088][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.089][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:41.091][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.092][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:41.094][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.095][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:41.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.099][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.100][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.101][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:41.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:41.104][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.105][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:41.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:41.108][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.110][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.111][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:41.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:41.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.120][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:41.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:41.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.125][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.129][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:41.130][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.143][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[2026-02-07 16:02:41.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.149][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[2026-02-07 16:02:41.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.189][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[2026-02-07 16:02:41.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.201][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[2026-02-07 16:02:41.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.212][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[2026-02-07 16:02:41.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.228][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[2026-02-07 16:02:41.229][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:41.234][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:41.236][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:41.238][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:41.240][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:41.242][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:41.244][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:41.246][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:41.248][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:41.250][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:41.252][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:41.254][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:41.256][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:41.257][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:41.259][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:41.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:41.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:41.265][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:41.267][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:41.269][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:41.271][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:41.272][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:41.274][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:41.276][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:41.278][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:41.279][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:41.281][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:41.283][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:41.285][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:41.287][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:41.289][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:41.291][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:41.292][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:41.294][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:41.296][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:41.298][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:41.300][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:41.302][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:41.304][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:41.305][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:41.307][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:41.310][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:41.312][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:41.313][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:41.315][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:41.317][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:41.319][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:41.321][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:41.323][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:41.325][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:41.327][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:41.328][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:41.330][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:41.332][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:41.334][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:41.336][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:41.337][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:41.339][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:41.341][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:41.343][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:41.345][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:41.347][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:41.349][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:41.351][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:41.352][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:41.354][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:41.356][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:41.358][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:41.360][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:41.362][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:41.364][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:41.365][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:41.367][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:41.369][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:41.371][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:41.373][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:41.375][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:41.377][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:41.378][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:41.380][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:41.382][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:41.384][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:41.386][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:41.393][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:41.396][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:41.399][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:41.401][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.403][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.441][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[2026-02-07 16:02:41.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.449][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[2026-02-07 16:02:41.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.503][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[2026-02-07 16:02:41.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.510][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[2026-02-07 16:02:41.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:41.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:41.544][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:41.557][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-07 16:02:41.559][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.560][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-07 16:02:41.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:41.564][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.565][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-07 16:02:41.567][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.568][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.569][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-07 16:02:41.570][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:41.572][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.573][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-07 16:02:41.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-07 16:02:41.576][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-07 16:02:41.577][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:41.578][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.579][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:41.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.583][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:41.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:41.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:41.586][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:41.588][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:41.588][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:41.588][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-07 16:02:41.588][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-07 16:02:41.589][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:41.590][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:41.591][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:41.593][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:41.600][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-07 16:02:41.623][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-07 16:02:41.640][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-07 16:02:41.650][biodb::testThat]
biodb.INFO [2026-02-07 16:02:41.651][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-07 16:02:41.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:41.654][biodb::testThat]
biodb.TRACE[2026-02-07 16:02:41.658][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-02-07 16:02:41.660][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:41.664][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-07 16:02:41.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:41.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:41.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:41.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:41.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:41.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:41.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:41.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:41.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:41.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:41.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:41.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:41.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:41.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:41.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:41.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:41.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:41.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:41.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:41.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.832][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.837][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.847][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:41.927][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-02-07 16:02:41.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:41.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:41.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:41.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.940][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:41.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:41.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.945][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:41.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:41.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.977][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:41.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:41.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:41.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:41.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.021][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.026][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.031][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.060][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.063][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.064][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.082][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.097][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.099][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.100][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.101][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.134][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.138][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.170][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.171][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.172][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.174][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.213][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.214][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.215][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.233][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.235][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.236][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.237][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.244][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.245][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.247][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.248][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.255][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.256][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.257][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.259][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.267][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.268][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.269][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.276][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.278][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.279][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.280][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.304][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-02-07 16:02:42.355][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-02-07 16:02:42.356][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-02-07 16:02:42.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-07 16:02:42.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:42.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:42.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:42.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:42.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:42.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-07 16:02:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.457][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.554][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-07 16:02:42.601][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-02-07 16:02:42.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.634][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-07 16:02:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-07 16:02:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:42.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-07 16:02:42.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.644][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:42.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-07 16:02:42.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.712][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.717][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.724][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-02-07 16:02:42.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.766][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.768][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.769][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.770][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.787][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.793][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.803][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.804][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.805][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.807][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.808][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:42.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.824][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.839][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.841][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.842][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.843][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:42.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:42.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.877][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.880][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.881][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.882][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:42.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:42.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.919][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.921][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.922][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.923][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:42.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.956][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.957][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.959][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.960][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:42.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.992][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.993][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.995][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:42.996][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:42.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:42.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:43.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.013][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-07 16:02:43.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-07 16:02:43.016][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.017][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.023][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-07 16:02:43.025][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-07 16:02:43.026][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.027][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.034][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-07 16:02:43.035][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-07 16:02:43.036][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.038][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.044][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-07 16:02:43.046][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-07 16:02:43.047][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.048][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-07 16:02:43.056][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-07 16:02:43.057][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.058][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.065][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:43.067][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-02-07 16:02:43.068][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.069][ef$get] fields variable is a list.
biodb.TRACE[2026-02-07 16:02:43.076][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-07 16:02:43.077][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-07 16:02:43.079][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-07 16:02:43.080][ef$get] fields variable is a list.
biodb.INFO [2026-02-07 16:02:43.091][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.093][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-07 16:02:43.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.096][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:43.099][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-02-07 16:02:43.103][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-02-07 16:02:43.107][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:43.152][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-07 16:02:43.154][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-07 16:02:43.155][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-07 16:02:43.341][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.342][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-07 16:02:43.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.344][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.353][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.355][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-07 16:02:43.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.357][biodb::testThat]
biodb.WARN [2026-02-07 16:02:43.380][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-02-07 16:02:43.405][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-02-07 16:02:43.416][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.418][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-07 16:02:43.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.420][biodb::testThat]
biodb.DEBUG[2026-02-07 16:02:43.444][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-02-07 16:02:43.510][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-07 16:02:43.512][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-02-07 16:02:43.514][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-02-07 16:02:43.516][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-02-07 16:02:43.539][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-02-07 16:02:43.613][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.615][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-07 16:02:43.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.618][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.629][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.631][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-07 16:02:43.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.634][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.645][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.646][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:43.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.649][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.658][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.659][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-07 16:02:43.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-07 16:02:43.661][biodb::testThat]
biodb.INFO [2026-02-07 16:02:43.670][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:43.671][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-07 16:02:43.673][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:43.674][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:43.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:43.676][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:43.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:43.678][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-02-07 16:02:43.693][biodb::testContext]
biodb.INFO [2026-02-07 16:02:43.694][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:43.695][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-02-07 16:02:43.696][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-07 16:02:43.698][biodb::testContext]
biodb.INFO [2026-02-07 16:02:43.700][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:43.702][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:43.706][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:43.708][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-07 16:02:43.709][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.714][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-07 16:02:43.715][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.720][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-07 16:02:43.721][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.726][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-07 16:02:43.732][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-07 16:02:43.733][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-07 16:02:43.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.738][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-07 16:02:43.739][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-07 16:02:43.740][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.745][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-07 16:02:43.746][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-07 16:02:43.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.751][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-07 16:02:43.752][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-07 16:02:43.753][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-07 16:02:43.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.758][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-07 16:02:43.759][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.764][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-07 16:02:43.765][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-07 16:02:43.766][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-07 16:02:43.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.771][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:43.772][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-07 16:02:43.773][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-07 16:02:43.775][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-07 16:02:43.776][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-07 16:02:43.777][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-07 16:02:43.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.782][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-07 16:02:43.783][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-07 16:02:43.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.788][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-07 16:02:43.789][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-07 16:02:43.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.794][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-07 16:02:43.795][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-07 16:02:43.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.800][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-07 16:02:43.801][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-07 16:02:43.802][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-07 16:02:43.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.807][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-07 16:02:43.808][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-07 16:02:43.819][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-07 16:02:43.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.824][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-07 16:02:43.825][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-07 16:02:43.827][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-07 16:02:43.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.832][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-07 16:02:43.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.835][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-02-07 16:02:43.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:43.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.843][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.844][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:43.845][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:43.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.848][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-07 16:02:43.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:43.851][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.852][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.853][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:43.853][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:43.853][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:43.853][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:43.853][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:43.854][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:43.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:43.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.863][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.864][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:43.865][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:43.866][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.867][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.869][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-07 16:02:43.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.872][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:43.874][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:43.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.877][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.880][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.881][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:43.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:43.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.885][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-07 16:02:43.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.888][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.890][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-07 16:02:43.890][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-07 16:02:43.890][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-07 16:02:43.890][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-07 16:02:43.890][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-07 16:02:43.891][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:43.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.895][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:43.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.898][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.899][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.901][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:43.902][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:43.903][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.904][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.906][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-07 16:02:43.908][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.909][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-02-07 16:02:43.910][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.911][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:43.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.914][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.915][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.916][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-07 16:02:43.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:43.920][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.921][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-07 16:02:43.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.926][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.928][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:43.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.931][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:43.937][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.940][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.941][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.942][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:43.943][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:43.945][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.946][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.947][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-07 16:02:43.949][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.951][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-07 16:02:43.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:43.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.957][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.959][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-07 16:02:43.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:43.962][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.963][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-07 16:02:43.964][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:43.966][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.967][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:43.968][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-07 16:02:43.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:43.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:43.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:43.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:43.979][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:43.982][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:43.983][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:43.984][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:43.986][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:43.987][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:43.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:43.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:43.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:43.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:43.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:43.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:43.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.079][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-07 16:02:44.081][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-07 16:02:44.083][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-07 16:02:44.085][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-07 16:02:44.086][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-07 16:02:44.088][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-07 16:02:44.090][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:44.091][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:44.093][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-07 16:02:44.095][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-07 16:02:44.097][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-07 16:02:44.098][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-07 16:02:44.100][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-07 16:02:44.102][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-07 16:02:44.104][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-07 16:02:44.106][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-07 16:02:44.108][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-07 16:02:44.110][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-07 16:02:44.111][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-07 16:02:44.113][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-07 16:02:44.115][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-07 16:02:44.117][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-07 16:02:44.119][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-07 16:02:44.121][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-07 16:02:44.123][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-07 16:02:44.124][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-07 16:02:44.126][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-07 16:02:44.128][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-07 16:02:44.134][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-07 16:02:44.136][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-07 16:02:44.137][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-07 16:02:44.139][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-07 16:02:44.141][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-07 16:02:44.142][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-07 16:02:44.144][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-07 16:02:44.146][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-07 16:02:44.147][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-07 16:02:44.149][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-07 16:02:44.151][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-07 16:02:44.152][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-07 16:02:44.154][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-07 16:02:44.156][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-07 16:02:44.157][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-07 16:02:44.159][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-07 16:02:44.161][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-07 16:02:44.163][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-07 16:02:44.164][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-07 16:02:44.166][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-07 16:02:44.168][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-07 16:02:44.169][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-07 16:02:44.171][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-07 16:02:44.173][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-07 16:02:44.174][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-07 16:02:44.176][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-07 16:02:44.178][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-07 16:02:44.179][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-07 16:02:44.181][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-07 16:02:44.183][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-07 16:02:44.185][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-07 16:02:44.186][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-07 16:02:44.188][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-07 16:02:44.190][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-07 16:02:44.191][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-07 16:02:44.193][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-07 16:02:44.195][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-07 16:02:44.196][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-07 16:02:44.198][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-07 16:02:44.200][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-07 16:02:44.202][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-07 16:02:44.203][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-07 16:02:44.205][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-07 16:02:44.207][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-07 16:02:44.208][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-07 16:02:44.210][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-07 16:02:44.212][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-07 16:02:44.214][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-07 16:02:44.215][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-07 16:02:44.217][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-07 16:02:44.219][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-07 16:02:44.220][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-07 16:02:44.222][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-07 16:02:44.224][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-07 16:02:44.225][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-07 16:02:44.227][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-07 16:02:44.229][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-07 16:02:44.230][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-07 16:02:44.232][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.234][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.235][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[2026-02-07 16:02:44.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-07 16:02:44.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-07 16:02:44.365][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-02-07 16:02:44.367][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-02-07 16:02:44.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:44.371][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-02-07 16:02:44.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:44.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-07 16:02:44.374][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:44.375][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-02-07 16:02:44.377][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:44.378][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-07 16:02:44.379][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-02-07 16:02:44.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-07 16:02:44.382][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:44.383][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-02-07 16:02:44.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-02-07 16:02:44.385][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-02-07 16:02:44.387][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-07 16:02:44.388][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:44.389][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-07 16:02:44.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:44.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:44.393][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-07 16:02:44.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-07 16:02:44.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-07 16:02:44.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-07 16:02:44.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:44.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-02-07 16:02:44.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-02-07 16:02:44.398][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-02-07 16:02:44.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-07 16:02:44.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-07 16:02:44.401][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-07 16:02:44.402][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-07 16:02:44.404][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-02-07 16:02:44.408][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-02-07 16:02:44.412][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-02-07 16:02:44.413][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-07 16:02:44.414][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-02-07 16:02:44.415][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-07 16:02:44.416][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-07 16:02:44.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-07 16:02:44.419][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-07 16:02:44.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-07 16:02:44.421][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-07 16:02:44.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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)