Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-27 23:55 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-27 09:55 -0400 (Sat, 27 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
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_1.13.1.tar.gz
StartedAt: 2025-09-27 16:01:22 -0400 (Sat, 27 Sep 2025)
EndedAt: 2025-09-27 16:02:22 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 60.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "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)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-09-27 16:02:19.768][biodb::testContext]
biodb.INFO [2025-09-27 16:02:19.771][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:19.772][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-27 16:02:19.772][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:19.773][biodb::testContext]
biodb.INFO [2025-09-27 16:02:19.778][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:19.779][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:19.785][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:19.785][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-27 16:02:19.786][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.789][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-27 16:02:19.803][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.806][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-27 16:02:19.807][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.809][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-27 16:02:19.810][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-27 16:02:19.819][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-27 16:02:19.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.822][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-27 16:02:19.823][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-27 16:02:19.824][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.827][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-27 16:02:19.828][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-27 16:02:19.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.831][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-27 16:02:19.831][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-27 16:02:19.832][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-27 16:02:19.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.835][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-27 16:02:19.836][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.839][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-27 16:02:19.840][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-27 16:02:19.841][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-27 16:02:19.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.844][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:19.844][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-27 16:02:19.845][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-27 16:02:19.846][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-27 16:02:19.847][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-27 16:02:19.848][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-27 16:02:19.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.850][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-27 16:02:19.851][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-27 16:02:19.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.854][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-27 16:02:19.855][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-27 16:02:19.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.858][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-27 16:02:19.859][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-27 16:02:19.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.861][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-27 16:02:19.862][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-27 16:02:19.863][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-27 16:02:19.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.866][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:19.866][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-27 16:02:19.885][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-27 16:02:19.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:19.888][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-27 16:02:19.889][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-27 16:02:19.890][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-27 16:02:19.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:19.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:19.892][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[2025-09-27 16:02:19.894][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-27 16:02:19.917][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.929][self$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[2025-09-27 16:02:19.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:19.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.932][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.933][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.934][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.934][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:19.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:19.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.937][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-27 16:02:19.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:19.938][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.939][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.940][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:19.940][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:19.940][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:19.940][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:19.940][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:19.941][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:19.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:19.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.946][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:19.947][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:19.948][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.948][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.949][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-27 16:02:19.951][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.951][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:19.952][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.953][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:19.954][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.955][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.955][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.957][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:19.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:19.958][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.963][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-27 16:02:19.964][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:19.965][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.965][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.966][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:19.966][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:19.966][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:19.966][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:19.966][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:19.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:19.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:19.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.972][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.972][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:19.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:19.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.975][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.976][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-27 16:02:19.977][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.978][self$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[2025-09-27 16:02:19.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:19.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.982][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.984][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:19.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:19.985][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.986][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-27 16:02:19.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:19.988][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:19.989][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:19.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:19.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:19.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:19.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:19.995][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:19.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:19.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:19.998][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:19.999][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-27 16:02:20.000][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.001][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:20.002][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.003][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:20.004][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:20.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:20.007][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:20.007][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:20.008][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.009][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-27 16:02:20.010][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:20.011][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.011][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.012][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:20.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:20.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:20.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:20.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:20.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:20.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:20.018][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.018][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:20.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:20.020][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.021][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.024][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:20.024][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.083][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-27 16:02:20.086][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-27 16:02:20.087][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-27 16:02:20.088][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-27 16:02:20.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-27 16:02:20.090][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:02:20.092][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:20.097][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:20.098][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-27 16:02:20.099][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:02:20.100][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:02:20.101][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-27 16:02:20.102][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:20.103][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:20.104][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-27 16:02:20.105][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:02:20.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-27 16:02:20.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-27 16:02:20.108][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-27 16:02:20.109][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-27 16:02:20.110][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-27 16:02:20.111][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-27 16:02:20.112][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-27 16:02:20.113][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-27 16:02:20.114][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-27 16:02:20.115][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-27 16:02:20.116][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-27 16:02:20.118][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-27 16:02:20.119][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-27 16:02:20.120][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-27 16:02:20.121][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-27 16:02:20.122][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-27 16:02:20.123][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-27 16:02:20.124][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-27 16:02:20.125][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-27 16:02:20.126][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-27 16:02:20.127][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-27 16:02:20.128][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-27 16:02:20.129][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-27 16:02:20.130][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-27 16:02:20.131][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-27 16:02:20.132][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-27 16:02:20.133][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-27 16:02:20.134][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-27 16:02:20.136][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-27 16:02:20.137][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-27 16:02:20.138][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-27 16:02:20.139][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-27 16:02:20.140][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-27 16:02:20.141][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-27 16:02:20.142][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-27 16:02:20.143][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-27 16:02:20.144][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-27 16:02:20.145][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-27 16:02:20.147][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-27 16:02:20.148][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-27 16:02:20.149][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-27 16:02:20.150][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-27 16:02:20.151][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-27 16:02:20.152][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-27 16:02:20.153][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-27 16:02:20.154][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-27 16:02:20.155][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-27 16:02:20.156][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-27 16:02:20.157][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-27 16:02:20.159][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-27 16:02:20.160][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-27 16:02:20.161][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-27 16:02:20.162][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-27 16:02:20.163][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-27 16:02:20.164][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-27 16:02:20.166][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-27 16:02:20.167][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-27 16:02:20.168][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-27 16:02:20.169][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-27 16:02:20.170][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-27 16:02:20.171][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-27 16:02:20.173][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-27 16:02:20.174][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-27 16:02:20.175][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-27 16:02:20.176][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-27 16:02:20.177][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-27 16:02:20.178][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-27 16:02:20.183][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-27 16:02:20.185][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:20.187][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:20.188][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.190][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.208][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[2025-09-27 16:02:20.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.213][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[2025-09-27 16:02:20.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:20.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:20.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.292][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[2025-09-27 16:02:20.295][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:20.303][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-27 16:02:20.305][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.306][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-27 16:02:20.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:20.308][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.309][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-27 16:02:20.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:20.312][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-27 16:02:20.312][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:20.313][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.314][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-27 16:02:20.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-27 16:02:20.316][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-27 16:02:20.317][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:20.318][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.318][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-27 16:02:20.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:20.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:20.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:20.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:20.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:20.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:20.324][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:02:20.324][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:02:20.324][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-27 16:02:20.324][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-27 16:02:20.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:20.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:20.326][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:20.327][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:20.331][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-27 16:02:20.349][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-27 16:02:20.361][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-27 16:02:20.369][biodb::testThat]
biodb.INFO [2025-09-27 16:02:20.370][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-27 16:02:20.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:20.372][biodb::testThat]
biodb.TRACE[2025-09-27 16:02:20.375][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-09-27 16:02:20.376][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-27 16:02:20.385][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-27 16:02:20.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-27 16:02:20.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-27 16:02:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.457][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.481][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.484][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.490][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:02:20.543][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-09-27 16:02:20.546][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:20.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:20.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:20.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:20.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:20.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:20.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:20.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.638][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.641][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.644][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.666][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.686][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.687][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.689][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.689][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.710][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.711][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.712][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.734][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.760][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.761][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.762][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.773][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.776][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.780][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.781][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.783][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.790][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.798][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.803][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.804][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.806][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.823][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-09-27 16:02:20.864][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-27 16:02:20.865][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-27 16:02:20.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-27 16:02:20.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:20.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:20.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:20.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:20.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:20.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-27 16:02:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.913][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.917][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:20.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.921][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:20.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:20.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:20.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:20.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:20.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:20.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.978][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.988][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:20.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:20.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:20.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:20.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:20.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-27 16:02:21.010][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-09-27 16:02:21.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:21.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:21.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-27 16:02:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-27 16:02:21.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.032][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:21.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-27 16:02:21.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.035][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:21.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-27 16:02:21.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.046][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.078][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.081][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.084][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-27 16:02:21.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.111][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.112][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.113][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.128][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.131][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.134][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.135][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.136][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.137][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.158][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.159][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.160][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.186][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.188][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.189][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.209][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.210][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.212][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.233][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.233][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.235][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.255][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.256][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.257][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.268][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-27 16:02:21.269][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-27 16:02:21.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.271][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.275][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.276][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-27 16:02:21.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.277][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.282][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-27 16:02:21.283][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-27 16:02:21.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.284][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-27 16:02:21.290][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-27 16:02:21.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.292][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.300][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.301][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-27 16:02:21.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.303][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.308][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.309][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-27 16:02:21.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.310][ef$get] fields variable is a list.
biodb.TRACE[2025-09-27 16:02:21.314][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-27 16:02:21.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-27 16:02:21.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-27 16:02:21.317][ef$get] fields variable is a list.
biodb.INFO [2025-09-27 16:02:21.324][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.324][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-27 16:02:21.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.326][biodb::testThat]
biodb.DEBUG[2025-09-27 16:02:21.327][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-09-27 16:02:21.330][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-09-27 16:02:21.332][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:21.353][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-27 16:02:21.355][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-27 16:02:21.356][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-27 16:02:21.387][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.388][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-27 16:02:21.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.390][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.395][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.396][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-27 16:02:21.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.403][biodb::testThat]
biodb.WARN [2025-09-27 16:02:21.418][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-27 16:02:21.433][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-27 16:02:21.441][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.442][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-27 16:02:21.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.444][biodb::testThat]
biodb.DEBUG[2025-09-27 16:02:21.456][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-09-27 16:02:21.495][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-27 16:02:21.496][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-27 16:02:21.497][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-27 16:02:21.498][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-27 16:02:21.507][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-27 16:02:21.528][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.529][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-27 16:02:21.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.531][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.538][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.539][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-27 16:02:21.540][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.541][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.548][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.549][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-27 16:02:21.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.551][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.558][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.559][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-27 16:02:21.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-27 16:02:21.560][biodb::testThat]
biodb.INFO [2025-09-27 16:02:21.567][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-27 16:02:21.568][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-27 16:02:21.569][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-27 16:02:21.569][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.571][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.572][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-27 16:02:21.585][biodb::testContext]
biodb.INFO [2025-09-27 16:02:21.586][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:21.587][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-09-27 16:02:21.588][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-27 16:02:21.589][biodb::testContext]
biodb.INFO [2025-09-27 16:02:21.590][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:21.592][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:21.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:21.596][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-27 16:02:21.597][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.599][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-27 16:02:21.600][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.603][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-27 16:02:21.604][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.607][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-27 16:02:21.607][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-27 16:02:21.608][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-27 16:02:21.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.611][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-27 16:02:21.612][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-27 16:02:21.613][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.616][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-27 16:02:21.617][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-27 16:02:21.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.620][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-27 16:02:21.620][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-27 16:02:21.621][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-27 16:02:21.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.624][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-27 16:02:21.625][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.628][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-27 16:02:21.629][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-27 16:02:21.630][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-27 16:02:21.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.632][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[2025-09-27 16:02:21.633][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:21.633][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-27 16:02:21.634][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-27 16:02:21.635][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-27 16:02:21.636][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-27 16:02:21.636][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-27 16:02:21.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.639][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-27 16:02:21.640][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-27 16:02:21.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.642][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-27 16:02:21.643][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-27 16:02:21.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.646][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-27 16:02:21.647][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-27 16:02:21.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.649][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-27 16:02:21.650][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-27 16:02:21.651][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-27 16:02:21.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.653][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-27 16:02:21.654][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-27 16:02:21.671][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-27 16:02:21.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-27 16:02:21.675][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-27 16:02:21.675][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-27 16:02:21.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.678][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-27 16:02:21.680][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.680][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-27 16:02:21.681][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.682][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:21.683][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.683][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.684][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.685][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.686][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:21.686][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:21.687][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.688][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-27 16:02:21.688][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:21.689][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.690][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.691][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:21.691][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:21.691][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:21.691][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:21.691][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:21.695][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:21.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.698][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:21.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.700][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.700][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:21.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:21.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.703][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.704][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-27 16:02:21.705][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.706][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:21.707][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.707][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:21.708][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.709][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.710][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.711][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.712][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:21.712][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:21.713][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.714][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-27 16:02:21.714][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:21.715][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.716][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-27 16:02:21.717][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:21.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.720][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:21.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.723][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:21.724][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:21.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.726][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.727][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-27 16:02:21.728][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.729][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-27 16:02:21.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:21.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.733][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.734][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.734][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-27 16:02:21.735][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:21.736][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.737][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-27 16:02:21.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:21.738][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.739][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.740][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.741][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:21.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.743][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:21.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.745][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.746][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.747][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:21.748][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:21.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.749][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.750][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-27 16:02:21.751][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.752][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-27 16:02:21.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.753][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:21.754][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.755][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.756][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.757][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-27 16:02:21.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:21.759][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.760][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-27 16:02:21.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:21.761][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:21.762][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.763][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-27 16:02:21.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:21.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:21.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:21.767][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:21.769][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:21.770][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:21.771][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:21.772][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:21.773][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:21.774][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.810][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[2025-09-27 16:02:21.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.827][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[2025-09-27 16:02:21.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.834][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[2025-09-27 16:02:21.835][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-27 16:02:21.836][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-27 16:02:21.837][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-27 16:02:21.839][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-27 16:02:21.840][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-27 16:02:21.841][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-27 16:02:21.842][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:21.843][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:21.844][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-27 16:02:21.845][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-27 16:02:21.846][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-27 16:02:21.848][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-27 16:02:21.849][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-27 16:02:21.850][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-27 16:02:21.851][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-27 16:02:21.852][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-27 16:02:21.853][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-27 16:02:21.854][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-27 16:02:21.855][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-27 16:02:21.856][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-27 16:02:21.857][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-27 16:02:21.858][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-27 16:02:21.859][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-27 16:02:21.860][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-27 16:02:21.861][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-27 16:02:21.862][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-27 16:02:21.863][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-27 16:02:21.865][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-27 16:02:21.866][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-27 16:02:21.867][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-27 16:02:21.868][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-27 16:02:21.869][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-27 16:02:21.870][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-27 16:02:21.871][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-27 16:02:21.872][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-27 16:02:21.873][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-27 16:02:21.874][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-27 16:02:21.876][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-27 16:02:21.877][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-27 16:02:21.882][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-27 16:02:21.883][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-27 16:02:21.884][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-27 16:02:21.885][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-27 16:02:21.887][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-27 16:02:21.888][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-27 16:02:21.889][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-27 16:02:21.890][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-27 16:02:21.891][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-27 16:02:21.892][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-27 16:02:21.893][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-27 16:02:21.894][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-27 16:02:21.895][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-27 16:02:21.896][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-27 16:02:21.897][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-27 16:02:21.899][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-27 16:02:21.900][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-27 16:02:21.901][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-27 16:02:21.902][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-27 16:02:21.903][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-27 16:02:21.904][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-27 16:02:21.905][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-27 16:02:21.906][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-27 16:02:21.908][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-27 16:02:21.909][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-27 16:02:21.910][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-27 16:02:21.911][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-27 16:02:21.912][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-27 16:02:21.913][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-27 16:02:21.914][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-27 16:02:21.915][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-27 16:02:21.916][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-27 16:02:21.917][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-27 16:02:21.919][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-27 16:02:21.920][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-27 16:02:21.921][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-27 16:02:21.922][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-27 16:02:21.923][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-27 16:02:21.924][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-27 16:02:21.925][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-27 16:02:21.926][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-27 16:02:21.928][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-27 16:02:21.929][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-27 16:02:21.930][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-27 16:02:21.935][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-27 16:02:21.936][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-09-27 16:02:21.937][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-27 16:02:21.938][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.939][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.960][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[2025-09-27 16:02:21.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.978][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[2025-09-27 16:02:21.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.983][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[2025-09-27 16:02:21.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.989][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[2025-09-27 16:02:21.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:21.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:21.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:21.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:21.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:21.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:21.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:21.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-27 16:02:22.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-27 16:02:22.025][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-27 16:02:22.026][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-27 16:02:22.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.028][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-27 16:02:22.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-27 16:02:22.031][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.031][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-27 16:02:22.032][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.034][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-27 16:02:22.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-27 16:02:22.035][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.036][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-27 16:02:22.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-27 16:02:22.038][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-27 16:02:22.039][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.040][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-27 16:02:22.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-27 16:02:22.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-27 16:02:22.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-27 16:02:22.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-27 16:02:22.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:02:22.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-27 16:02:22.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-27 16:02:22.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-27 16:02:22.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-27 16:02:22.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-27 16:02:22.048][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-27 16:02:22.049][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-27 16:02:22.050][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-27 16:02:22.052][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-27 16:02:22.056][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-27 16:02:22.057][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-27 16:02:22.058][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-27 16:02:22.058][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-27 16:02:22.059][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-27 16:02:22.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-27 16:02:22.060][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-27 16:02:22.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-27 16:02:22.062][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-27 16:02:22.063][FUN] Functions in observer 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_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)