Back to Long Tests report for BioC 3.21

This page was generated on 2025-10-11 23:55 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-11 09:55 -0400 (Sat, 11 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbNci on 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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-10-11 16:01:14 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 16:02:38 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 83.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-10-11 16:02:33.742][biodb::testContext]
biodb.INFO [2025-10-11 16:02:33.746][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:33.747][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-11 16:02:33.748][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:33.749][biodb::testContext]
biodb.INFO [2025-10-11 16:02:33.756][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:33.758][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:33.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:33.768][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:33.769][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.774][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:33.800][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.805][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:33.807][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.812][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:33.813][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:33.814][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:33.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.828][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:33.829][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:33.831][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.835][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:33.836][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:33.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.841][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:33.842][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:33.843][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:33.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.848][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:33.849][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.854][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:33.855][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:33.856][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:33.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.861][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:33.862][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:33.863][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:33.865][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:33.866][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:33.867][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:33.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.872][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:33.873][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:33.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.878][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:33.879][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:33.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.883][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:33.885][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:33.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.889][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:33.890][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:33.892][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:33.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.896][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:33.897][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:33.908][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:33.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.913][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:33.914][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:33.915][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:33.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:33.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:33.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:33.922][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:33.965][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:33.987][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:02:33.989][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:33.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:33.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:33.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:33.994][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:33.995][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:33.997][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:33.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:33.999][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.000][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:34.002][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:34.003][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.004][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.005][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:34.005][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:34.005][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:34.005][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:34.005][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:34.007][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:34.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:34.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.015][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:34.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:34.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.020][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.021][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:34.023][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.024][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:34.026][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.027][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:34.028][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.029][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.031][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.033][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:34.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:34.035][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.037][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:34.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:34.044][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.046][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:34.046][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:34.046][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:34.046][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:34.046][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:34.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:34.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:34.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.056][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:34.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:34.059][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.061][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.062][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:34.064][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.065][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:02:34.067][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.068][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:34.069][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.070][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.072][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.073][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.074][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:34.075][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:34.077][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.078][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:34.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:34.080][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.083][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:34.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:34.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.092][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:34.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:34.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.097][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.098][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:34.101][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:34.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:34.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.111][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:34.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:34.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.115][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:34.116][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:34.117][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.120][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:34.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:34.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.129][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:34.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:34.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.134][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.138][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:34.139][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.231][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:34.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:34.238][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:34.240][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:34.242][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:34.243][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:34.245][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:34.250][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:34.252][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:34.254][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:34.256][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:34.257][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:34.259][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:34.261][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:34.262][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:34.264][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:34.266][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:34.267][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:34.269][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:34.271][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:34.272][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:34.274][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:34.276][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:34.278][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:34.279][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:34.281][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:34.283][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:34.284][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:34.286][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:34.288][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:34.289][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:34.291][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:34.293][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:34.294][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:34.296][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:34.298][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:34.299][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:34.301][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:34.303][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:34.305][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:34.306][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:34.308][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:34.310][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:34.311][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:34.313][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:34.315][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:34.316][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:34.318][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:34.320][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:34.321][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:34.323][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:34.325][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:34.327][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:34.328][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:34.330][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:34.332][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:34.333][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:34.335][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:34.337][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:34.338][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:34.340][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:34.342][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:34.343][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:34.345][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:34.347][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:34.348][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:34.350][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:34.352][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:34.354][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:34.355][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:34.357][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:34.359][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:34.360][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:34.362][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:34.364][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:34.365][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:34.367][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:34.369][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:34.371][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:34.372][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:34.374][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:34.376][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:34.377][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:34.385][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:34.387][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:34.390][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:34.391][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.393][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.449][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[2025-10-11 16:02:34.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.457][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[2025-10-11 16:02:34.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.465][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[2025-10-11 16:02:34.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.503][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[2025-10-11 16:02:34.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.518][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[2025-10-11 16:02:34.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:34.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:34.528][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:34.541][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:02:34.543][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.545][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:02:34.546][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.547][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:34.548][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.550][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:02:34.551][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.552][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.553][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:02:34.554][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:34.556][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.557][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:02:34.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:02:34.559][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:02:34.561][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:34.562][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.563][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:34.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:34.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:34.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:34.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:34.571][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:34.571][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:34.571][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:02:34.571][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:02:34.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:34.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:34.575][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:34.576][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:34.584][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:02:34.605][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:02:34.622][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:02:34.632][biodb::testThat]
biodb.INFO [2025-10-11 16:02:34.634][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-11 16:02:34.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:34.636][biodb::testThat]
biodb.TRACE[2025-10-11 16:02:34.640][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-11 16:02:34.642][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:34.646][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:02:34.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:34.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:34.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:34.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:34.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:34.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:34.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:34.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:34.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:34.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:34.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:34.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:34.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:34.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:34.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:34.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:34.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:34.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.811][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:34.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:34.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:34.907][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-11 16:02:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:34.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:34.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.915][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:34.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:34.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:34.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:34.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:34.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.028][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.116][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.121][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.150][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.151][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.154][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.186][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.189][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.220][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.222][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.224][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.256][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.257][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.259][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.296][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.297][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.299][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.316][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.317][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.320][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.328][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.330][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.341][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.347][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.351][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.357][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.359][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.361][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.385][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-11 16:02:35.438][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-11 16:02:35.439][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-11 16:02:35.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-11 16:02:35.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:35.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:35.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:35.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:35.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:35.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-11 16:02:35.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.507][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:35.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.597][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.603][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-11 16:02:35.649][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-11 16:02:35.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:35.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-11 16:02:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-11 16:02:35.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.687][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:35.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-11 16:02:35.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:35.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-11 16:02:35.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.748][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.794][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.799][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.804][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-11 16:02:35.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.846][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.847][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.849][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:35.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:35.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.865][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.880][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.882][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.884][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.885][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:35.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.915][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.919][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:35.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:35.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.939][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.949][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.951][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.957][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:35.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.988][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.989][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.992][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:35.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:35.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:35.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.023][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.025][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.027][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.058][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.060][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.062][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.078][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-11 16:02:36.080][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-11 16:02:36.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.082][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.089][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-11 16:02:36.090][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-11 16:02:36.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.093][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.099][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-11 16:02:36.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-11 16:02:36.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.103][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.109][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-11 16:02:36.111][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-11 16:02:36.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.113][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-11 16:02:36.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.127][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.133][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:36.135][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-11 16:02:36.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.137][ef$get] fields variable is a list.
biodb.TRACE[2025-10-11 16:02:36.144][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-11 16:02:36.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-11 16:02:36.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-11 16:02:36.147][ef$get] fields variable is a list.
biodb.INFO [2025-10-11 16:02:36.157][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.159][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-11 16:02:36.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.161][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:36.164][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-11 16:02:36.167][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-11 16:02:36.171][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:36.212][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:02:36.214][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:02:36.215][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:02:36.268][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.270][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-11 16:02:36.271][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.272][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.280][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.282][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-11 16:02:36.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.284][biodb::testThat]
biodb.WARN [2025-10-11 16:02:36.315][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-11 16:02:36.342][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-11 16:02:36.354][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.355][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-11 16:02:36.357][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.358][biodb::testThat]
biodb.DEBUG[2025-10-11 16:02:36.382][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-11 16:02:36.453][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-11 16:02:36.455][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-11 16:02:36.457][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-11 16:02:36.459][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-11 16:02:36.477][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-11 16:02:36.510][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.511][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-11 16:02:36.513][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.514][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.523][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.524][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-11 16:02:36.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.527][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.536][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.537][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:36.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.539][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.547][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.549][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-11 16:02:36.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-11 16:02:36.551][biodb::testThat]
biodb.INFO [2025-10-11 16:02:36.559][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:36.560][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:02:36.561][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:36.562][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:36.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:36.565][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.567][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-11 16:02:36.580][biodb::testContext]
biodb.INFO [2025-10-11 16:02:36.581][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:36.583][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-11 16:02:36.588][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-11 16:02:36.589][biodb::testContext]
biodb.INFO [2025-10-11 16:02:36.591][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:36.593][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:36.597][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:36.599][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-11 16:02:36.600][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.604][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-11 16:02:36.628][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.633][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-11 16:02:36.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.638][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-11 16:02:36.640][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-11 16:02:36.641][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-11 16:02:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.645][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-11 16:02:36.646][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-11 16:02:36.648][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.652][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-11 16:02:36.653][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-11 16:02:36.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.658][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-11 16:02:36.659][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-11 16:02:36.660][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-11 16:02:36.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.665][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-11 16:02:36.666][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.671][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-11 16:02:36.672][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-11 16:02:36.673][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-11 16:02:36.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.678][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:36.679][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-11 16:02:36.681][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-11 16:02:36.682][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-11 16:02:36.683][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-11 16:02:36.684][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-11 16:02:36.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.689][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-11 16:02:36.690][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-11 16:02:36.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.695][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-11 16:02:36.696][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-11 16:02:36.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.701][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-11 16:02:36.702][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-11 16:02:36.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.706][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-11 16:02:36.708][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-11 16:02:36.709][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-11 16:02:36.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.714][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-11 16:02:36.715][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-11 16:02:36.725][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-11 16:02:36.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.730][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-11 16:02:36.731][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-11 16:02:36.732][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-11 16:02:36.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.740][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-11 16:02:36.743][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.744][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-11 16:02:36.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:36.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.750][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.751][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.752][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:36.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:36.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.756][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-11 16:02:36.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:36.759][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.760][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.761][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:36.761][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:36.761][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:36.761][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:36.761][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:36.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:36.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:36.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.771][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:36.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:36.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.775][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.777][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-11 16:02:36.779][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.780][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:36.781][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:36.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.788][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.789][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:36.790][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:36.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.792][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-11 16:02:36.794][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:36.795][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.796][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.797][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-11 16:02:36.797][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-11 16:02:36.797][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-11 16:02:36.797][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-11 16:02:36.797][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-11 16:02:36.799][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:36.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:36.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.807][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:36.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:36.810][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.812][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.813][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-11 16:02:36.815][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.816][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-11 16:02:36.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.819][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:36.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.823][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.824][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.825][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-11 16:02:36.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:36.828][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.829][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-11 16:02:36.830][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:36.831][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.834][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:36.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:36.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.843][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:36.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:36.847][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.848][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.849][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-11 16:02:36.851][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.853][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-11 16:02:36.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:36.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.860][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.861][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-11 16:02:36.862][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:36.864][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.865][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-11 16:02:36.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:36.867][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:36.870][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.871][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-11 16:02:36.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:36.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:36.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:36.878][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:36.880][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:36.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:36.887][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:36.889][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:36.890][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:36.891][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.898][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[2025-10-11 16:02:36.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:36.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:36.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:36.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:36.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:36.990][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-11 16:02:36.992][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-11 16:02:36.994][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-11 16:02:36.996][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-11 16:02:36.998][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-11 16:02:37.000][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-11 16:02:37.002][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:37.004][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:37.006][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-11 16:02:37.008][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-11 16:02:37.010][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-11 16:02:37.012][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-11 16:02:37.015][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-11 16:02:37.017][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-11 16:02:37.024][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-11 16:02:37.026][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-11 16:02:37.027][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-11 16:02:37.029][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-11 16:02:37.031][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-11 16:02:37.033][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-11 16:02:37.034][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-11 16:02:37.036][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-11 16:02:37.038][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-11 16:02:37.039][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-11 16:02:37.041][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-11 16:02:37.043][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-11 16:02:37.049][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-11 16:02:37.051][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-11 16:02:37.053][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-11 16:02:37.055][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-11 16:02:37.056][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-11 16:02:37.058][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-11 16:02:37.060][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-11 16:02:37.062][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-11 16:02:37.092][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-11 16:02:37.094][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-11 16:02:37.095][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-11 16:02:37.097][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-11 16:02:37.106][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-11 16:02:37.108][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-11 16:02:37.110][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-11 16:02:37.111][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-11 16:02:37.113][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-11 16:02:37.115][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-11 16:02:37.126][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-11 16:02:37.128][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-11 16:02:37.130][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-11 16:02:37.131][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-11 16:02:37.133][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-11 16:02:37.135][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-11 16:02:37.137][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-11 16:02:37.139][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-11 16:02:37.140][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-11 16:02:37.142][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-11 16:02:37.144][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-11 16:02:37.151][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-11 16:02:37.153][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-11 16:02:37.155][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-11 16:02:37.156][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-11 16:02:37.158][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-11 16:02:37.160][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-11 16:02:37.162][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-11 16:02:37.164][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-11 16:02:37.165][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-11 16:02:37.167][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-11 16:02:37.169][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-11 16:02:37.170][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-11 16:02:37.172][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-11 16:02:37.174][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-11 16:02:37.176][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-11 16:02:37.177][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-11 16:02:37.179][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-11 16:02:37.181][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-11 16:02:37.182][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-11 16:02:37.184][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-11 16:02:37.186][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-11 16:02:37.188][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-11 16:02:37.189][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-11 16:02:37.191][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-11 16:02:37.193][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-11 16:02:37.194][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-11 16:02:37.196][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-11 16:02:37.198][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-11 16:02:37.200][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-11 16:02:37.202][initialize] This is biodb version 1.16.1.
biodb.DEBUG[2025-10-11 16:02:37.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-11 16:02:37.204][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.206][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.324][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[2025-10-11 16:02:37.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-11 16:02:37.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-11 16:02:37.351][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-11 16:02:37.353][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-11 16:02:37.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:37.357][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-11 16:02:37.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:37.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-11 16:02:37.361][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:37.362][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-11 16:02:37.363][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:37.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-11 16:02:37.366][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-11 16:02:37.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-11 16:02:37.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:37.370][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-11 16:02:37.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-11 16:02:37.372][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-11 16:02:37.374][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-11 16:02:37.375][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:37.376][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-11 16:02:37.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:37.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:37.380][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-11 16:02:37.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-11 16:02:37.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-11 16:02:37.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-11 16:02:37.385][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:37.385][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-11 16:02:37.385][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-11 16:02:37.385][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-11 16:02:37.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-11 16:02:37.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-11 16:02:37.388][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-11 16:02:37.390][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-11 16:02:37.391][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-11 16:02:37.395][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-11 16:02:37.399][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-11 16:02:37.405][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-11 16:02:37.407][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-11 16:02:37.408][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-11 16:02:37.409][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-11 16:02:37.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-11 16:02:37.411][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-11 16:02:37.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-11 16:02:37.414][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-11 16:02:37.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)