Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-13 23:55 -0500 (Sat, 13 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-13 09:55 -0500 (Sat, 13 Dec 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2025-12-13 16:01:59 -0500 (Sat, 13 Dec 2025)
EndedAt: 2025-12-13 16:03:20 -0500 (Sat, 13 Dec 2025)
EllapsedTime: 81.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-12-13 16:03:15.972][biodb::testContext]
biodb.INFO [2025-12-13 16:03:15.976][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:15.978][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-13 16:03:15.979][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:15.980][biodb::testContext]
biodb.INFO [2025-12-13 16:03:15.987][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:15.989][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:15.997][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:15.998][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:16.000][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.005][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:16.030][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.035][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:16.036][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.051][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:16.052][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:16.053][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:16.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.058][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:16.059][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:16.060][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.065][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:16.066][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:16.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.071][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:16.072][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:16.073][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:16.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.078][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:16.079][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.082][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[2025-12-13 16:03:16.083][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:16.085][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:16.086][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:16.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.091][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:16.092][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:16.093][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:16.094][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:16.096][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:16.097][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:16.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.101][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:16.103][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:16.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.107][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:16.109][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:16.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.113][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:16.114][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:16.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.119][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:16.120][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:16.122][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:16.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.126][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:16.127][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:16.138][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:16.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.143][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:16.144][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:16.146][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:16.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.152][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:16.195][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.217][self$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[2025-12-13 16:03:16.218][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:16.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.222][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.226][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:16.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:16.228][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.230][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:16.231][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:16.232][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.233][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.234][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:16.234][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:16.234][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:16.234][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:16.234][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:16.236][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:16.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.239][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:16.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.243][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.244][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.245][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:16.246][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:16.247][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.249][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.250][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:16.252][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.254][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:16.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:16.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.262][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:16.263][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:16.270][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.271][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:16.272][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:16.273][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.275][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.276][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:16.276][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:16.276][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:16.276][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:16.276][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:16.277][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:16.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.281][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:16.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.286][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:16.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:16.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.290][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.292][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:16.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.295][self$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[2025-12-13 16:03:16.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:16.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.300][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.304][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:16.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:16.307][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.308][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:16.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:16.310][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.313][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:16.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.319][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:16.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.324][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:16.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:16.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.329][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.330][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:16.332][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.334][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:16.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:16.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.339][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.341][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.342][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:16.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:16.345][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.346][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:16.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:16.349][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.351][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:16.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:16.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.361][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:16.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:16.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.366][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.370][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:16.371][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.464][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:16.469][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:16.471][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:16.473][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:16.475][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:16.476][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:16.478][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:16.484][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:16.486][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:16.488][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:16.490][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:16.491][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:16.493][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:16.495][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:16.497][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:16.499][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:16.500][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:16.502][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:16.504][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:16.505][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:16.507][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:16.509][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:16.511][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:16.512][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:16.514][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:16.516][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:16.518][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:16.520][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:16.521][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:16.523][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:16.525][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:16.527][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:16.529][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:16.531][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:16.533][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:16.535][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:16.537][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:16.538][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:16.540][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:16.542][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:16.544][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:16.546][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:16.547][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:16.549][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:16.551][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:16.553][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:16.555][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:16.556][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:16.558][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:16.560][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:16.562][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:16.564][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:16.565][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:16.567][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:16.569][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:16.571][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:16.573][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:16.574][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:16.576][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:16.578][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:16.580][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:16.582][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:16.584][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:16.586][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:16.588][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:16.590][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:16.592][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:16.594][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:16.595][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:16.597][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:16.599][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:16.601][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:16.603][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:16.605][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:16.607][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:16.609][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:16.611][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:16.612][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:16.614][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:16.616][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:16.618][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:16.620][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:16.622][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:16.630][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:16.632][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:16.636][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:16.637][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.640][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:16.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:16.782][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:16.795][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:16.798][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.799][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-13 16:03:16.801][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:16.803][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.804][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-13 16:03:16.806][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.808][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-13 16:03:16.810][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:16.811][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.812][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-13 16:03:16.814][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-13 16:03:16.815][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-13 16:03:16.816][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:16.818][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.819][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:16.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.822][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:16.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:16.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:16.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:16.827][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:16.827][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:16.827][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-13 16:03:16.827][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-13 16:03:16.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:16.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:16.831][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:16.832][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:16.840][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-13 16:03:16.863][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:16.880][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-13 16:03:16.890][biodb::testThat]
biodb.INFO [2025-12-13 16:03:16.891][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-13 16:03:16.892][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:16.894][biodb::testThat]
biodb.TRACE[2025-12-13 16:03:16.898][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-12-13 16:03:16.900][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:16.904][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-13 16:03:16.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:16.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:16.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:16.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:16.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:16.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:16.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:16.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:16.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:16.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:16.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:16.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:16.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:16.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:16.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:16.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.068][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.073][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.083][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:17.168][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-12-13 16:03:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:17.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.297][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.302][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.307][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.336][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.340][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.372][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.373][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.376][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.408][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.409][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.411][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.444][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.445][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.448][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.484][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.488][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.504][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.506][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.508][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.515][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.516][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.519][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.526][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.529][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.536][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.537][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.539][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.546][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.547][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.550][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.573][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-12-13 16:03:17.626][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-13 16:03:17.627][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-13 16:03:17.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-13 16:03:17.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:17.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:17.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:17.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:17.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:17.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-13 16:03:17.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.693][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:17.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:17.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:17.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:17.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:17.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:17.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:17.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.806][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-13 16:03:17.842][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-12-13 16:03:17.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-13 16:03:17.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.881][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-13 16:03:17.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:17.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-13 16:03:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.962][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-13 16:03:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:17.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:17.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:18.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:18.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.008][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:18.009][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:18.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.012][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:18.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.030][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.035][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.040][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.045][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.047][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.049][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.085][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.117][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.121][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.158][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.159][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.161][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.197][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.228][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.232][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.248][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-13 16:03:18.250][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-13 16:03:18.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.252][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.259][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.260][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-13 16:03:18.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.262][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.269][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-13 16:03:18.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-13 16:03:18.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.273][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-13 16:03:18.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-13 16:03:18.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.283][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.289][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.291][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-13 16:03:18.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.293][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.304][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.306][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-13 16:03:18.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.308][ef$get] fields variable is a list.
biodb.TRACE[2025-12-13 16:03:18.314][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-13 16:03:18.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-13 16:03:18.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-13 16:03:18.318][ef$get] fields variable is a list.
biodb.INFO [2025-12-13 16:03:18.329][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.330][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-13 16:03:18.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.332][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:18.335][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-12-13 16:03:18.338][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-12-13 16:03:18.341][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-13 16:03:18.380][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-13 16:03:18.382][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-13 16:03:18.383][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-13 16:03:18.567][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.568][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-13 16:03:18.570][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.571][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.579][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.581][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-13 16:03:18.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.583][biodb::testThat]
biodb.WARN [2025-12-13 16:03:18.614][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-13 16:03:18.641][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-13 16:03:18.654][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.655][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-13 16:03:18.656][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.657][biodb::testThat]
biodb.DEBUG[2025-12-13 16:03:18.680][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-12-13 16:03:18.749][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-13 16:03:18.751][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-13 16:03:18.753][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-13 16:03:18.755][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-13 16:03:18.772][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-13 16:03:18.843][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.844][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-13 16:03:18.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.847][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.857][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.858][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-13 16:03:18.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.860][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.875][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.876][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:18.877][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.879][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.887][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.888][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-13 16:03:18.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-13 16:03:18.891][biodb::testThat]
biodb.INFO [2025-12-13 16:03:18.899][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:18.901][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-13 16:03:18.902][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:18.903][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:18.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:18.905][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:18.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:18.907][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-13 16:03:18.922][biodb::testContext]
biodb.INFO [2025-12-13 16:03:18.923][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:18.924][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-12-13 16:03:18.925][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-13 16:03:18.927][biodb::testContext]
biodb.INFO [2025-12-13 16:03:18.929][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:18.931][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:18.936][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:18.937][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-13 16:03:18.939][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.943][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-13 16:03:18.945][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.949][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-13 16:03:18.950][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.955][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-13 16:03:18.956][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-13 16:03:18.957][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-13 16:03:18.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.962][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-13 16:03:18.963][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-13 16:03:18.964][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.969][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-13 16:03:18.970][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-13 16:03:18.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.975][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-13 16:03:18.976][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-13 16:03:18.977][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-13 16:03:18.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.982][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-13 16:03:18.983][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.987][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-13 16:03:18.989][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-13 16:03:18.990][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-13 16:03:18.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:18.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:18.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:18.994][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:18.996][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-13 16:03:18.997][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-13 16:03:18.998][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-13 16:03:18.999][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-13 16:03:19.001][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-13 16:03:19.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.005][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-13 16:03:19.007][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-13 16:03:19.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.011][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-13 16:03:19.012][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-13 16:03:19.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.021][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-13 16:03:19.023][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-13 16:03:19.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.027][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-13 16:03:19.029][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-13 16:03:19.030][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-13 16:03:19.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.034][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-13 16:03:19.036][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-13 16:03:19.046][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-13 16:03:19.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.050][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[2025-12-13 16:03:19.051][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-13 16:03:19.052][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-13 16:03:19.054][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-13 16:03:19.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.058][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-13 16:03:19.061][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.062][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-13 16:03:19.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:19.066][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.071][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:19.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:19.073][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.074][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-13 16:03:19.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:19.077][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.078][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.079][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:19.079][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:19.079][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:19.079][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:19.079][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:19.081][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:19.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.084][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:19.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.089][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.090][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:19.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:19.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.094][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.095][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-13 16:03:19.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.099][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:19.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:19.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.105][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.106][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.108][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:19.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:19.110][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.111][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-13 16:03:19.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:19.114][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.115][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.116][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-13 16:03:19.116][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-13 16:03:19.116][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-13 16:03:19.116][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-13 16:03:19.116][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-13 16:03:19.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:19.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:19.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.126][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.127][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:19.128][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:19.130][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.131][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.132][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-13 16:03:19.134][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.136][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-13 16:03:19.137][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.138][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:19.139][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.144][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-13 16:03:19.146][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:19.147][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.148][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-13 16:03:19.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:19.151][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.152][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.153][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:19.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:19.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.163][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:19.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:19.167][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.168][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.174][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-13 16:03:19.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-13 16:03:19.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:19.181][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.184][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-13 16:03:19.187][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:19.189][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.190][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-13 16:03:19.191][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:19.193][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.194][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.195][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.196][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-13 16:03:19.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:19.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.205][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.206][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:19.207][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:19.208][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.209][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:19.212][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.213][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[2025-12-13 16:03:19.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.287][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[2025-12-13 16:03:19.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.305][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-13 16:03:19.307][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-13 16:03:19.309][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-13 16:03:19.311][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-13 16:03:19.316][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-13 16:03:19.318][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-13 16:03:19.320][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:19.321][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:19.323][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-13 16:03:19.325][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-13 16:03:19.326][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-13 16:03:19.328][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-13 16:03:19.330][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-13 16:03:19.332][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-13 16:03:19.333][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-13 16:03:19.335][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-13 16:03:19.337][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-13 16:03:19.338][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-13 16:03:19.340][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-13 16:03:19.342][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-13 16:03:19.344][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-13 16:03:19.345][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-13 16:03:19.347][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-13 16:03:19.349][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-13 16:03:19.350][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-13 16:03:19.352][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-13 16:03:19.354][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-13 16:03:19.355][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-13 16:03:19.357][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-13 16:03:19.359][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-13 16:03:19.361][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-13 16:03:19.362][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-13 16:03:19.364][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-13 16:03:19.366][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-13 16:03:19.367][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-13 16:03:19.369][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-13 16:03:19.371][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-13 16:03:19.373][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-13 16:03:19.374][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-13 16:03:19.376][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-13 16:03:19.378][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-13 16:03:19.379][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-13 16:03:19.381][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-13 16:03:19.383][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-13 16:03:19.385][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-13 16:03:19.386][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-13 16:03:19.388][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-13 16:03:19.390][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-13 16:03:19.391][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-13 16:03:19.393][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-13 16:03:19.395][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-13 16:03:19.397][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-13 16:03:19.398][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-13 16:03:19.400][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-13 16:03:19.402][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-13 16:03:19.404][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-13 16:03:19.405][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-13 16:03:19.407][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-13 16:03:19.409][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-13 16:03:19.410][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-13 16:03:19.412][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-13 16:03:19.414][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-13 16:03:19.415][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-13 16:03:19.417][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-13 16:03:19.419][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-13 16:03:19.421][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-13 16:03:19.422][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-13 16:03:19.424][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-13 16:03:19.426][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-13 16:03:19.427][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-13 16:03:19.429][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-13 16:03:19.431][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-13 16:03:19.433][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-13 16:03:19.434][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-13 16:03:19.436][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-13 16:03:19.438][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-13 16:03:19.439][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-13 16:03:19.441][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-13 16:03:19.443][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-13 16:03:19.445][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-13 16:03:19.446][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-13 16:03:19.453][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-13 16:03:19.454][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-13 16:03:19.456][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-13 16:03:19.458][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-13 16:03:19.459][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-13 16:03:19.460][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.463][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-13 16:03:19.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-13 16:03:19.597][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-13 16:03:19.598][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:19.601][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.602][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-13 16:03:19.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-13 16:03:19.606][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.607][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-13 16:03:19.608][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.611][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-13 16:03:19.612][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-13 16:03:19.613][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.615][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-13 16:03:19.616][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-13 16:03:19.617][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-13 16:03:19.619][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-13 16:03:19.620][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.621][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-13 16:03:19.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-13 16:03:19.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-13 16:03:19.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-13 16:03:19.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-13 16:03:19.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:19.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-13 16:03:19.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-13 16:03:19.629][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-13 16:03:19.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-13 16:03:19.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-13 16:03:19.633][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-13 16:03:19.634][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-13 16:03:19.636][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-13 16:03:19.640][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-13 16:03:19.644][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-13 16:03:19.645][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-13 16:03:19.647][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-13 16:03:19.648][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-13 16:03:19.649][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-13 16:03:19.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-13 16:03:19.651][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-13 16:03:19.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-13 16:03:19.653][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-13 16:03:19.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbNci.Rcheck/00install.out

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