Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4853
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4640
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CHECK results for biodbNcbi on lconway

To the developers/maintainers of the biodbNcbi 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: biodbNcbi

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.13.1.tar.gz

StartedAt: 2025-10-04 16:01:15 -0400 (Sat, 04 Oct 2025)

EndedAt: 2025-10-04 16:02:17 -0400 (Sat, 04 Oct 2025)

EllapsedTime: 62.6 seconds

RetCode: 1

Status: ERROR

CheckDir: biodbNcbi.Rcheck

Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-10-04 16:02:09.998][biodb::testContext]
biodb.INFO [2025-10-04 16:02:10.001][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:10.002][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-10-04 16:02:10.003][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:10.004][biodb::testContext]
biodb.INFO [2025-10-04 16:02:10.009][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:10.010][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:10.016][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:10.017][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:10.018][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.021][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:10.035][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.038][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:10.039][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.050][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:10.051][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:10.052][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:10.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.055][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:10.056][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:10.057][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.060][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:10.061][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:10.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.064][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:10.064][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:10.065][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:10.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.068][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:10.069][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.072][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:10.073][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:10.073][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:10.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.076][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:10.077][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:10.078][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:10.078][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:10.079][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:10.080][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:10.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.082][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[2025-10-04 16:02:10.083][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:10.084][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:10.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.087][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:10.088][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:10.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.091][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:10.091][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:10.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.094][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:10.095][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:10.096][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:10.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.099][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:10.100][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:10.122][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:10.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.125][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:10.126][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:10.126][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:10.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.131][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:10.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.168][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:02:10.169][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.170][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.171][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:10.175][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.175][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.176][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:10.177][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.178][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.178][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.179][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:10.179][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:10.179][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:10.179][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:10.179][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:10.180][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:10.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.184][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.185][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.186][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.187][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.187][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.188][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.189][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:10.190][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.191][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:10.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.194][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.194][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.200][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.201][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:10.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.203][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.204][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:10.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.205][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:10.206][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:10.207][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:10.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.209][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.210][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.212][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.213][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.214][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.214][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.215][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.216][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.216][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:10.218][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.219][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:02:10.220][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.220][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.221][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.222][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.223][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.224][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:10.225][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.226][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.227][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:10.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.228][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.229][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.230][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.231][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:10.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.236][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.239][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.240][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:10.242][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.243][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:10.243][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.244][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.245][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.246][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.248][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.248][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:10.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.250][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.251][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:10.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.252][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.254][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.254][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:10.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.261][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.262][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.263][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.264][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.265][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.266][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:10.270][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.298][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[2025-10-04 16:02:10.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.335][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:10.339][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:10.340][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:10.346][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:10.347][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:10.348][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:10.349][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:10.350][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:10.351][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:10.353][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:10.354][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:10.355][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:10.356][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:10.357][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:10.358][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:10.359][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:10.361][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:10.362][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:10.363][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:10.364][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:10.365][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:10.366][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:10.368][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:10.369][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:10.370][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:10.371][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:10.372][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:10.373][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:10.374][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:10.376][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:10.377][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:10.378][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:10.379][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:10.380][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:10.381][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:10.382][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:10.384][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:10.385][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:10.386][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:10.387][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:10.389][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:10.390][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:10.391][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:10.392][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:10.393][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:10.394][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:10.395][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:10.397][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:10.398][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:10.399][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:10.400][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:10.401][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:10.402][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:10.403][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:10.404][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:10.406][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:10.407][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:10.408][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:10.409][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:10.410][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:10.411][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:10.412][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:10.414][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:10.415][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:10.416][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:10.417][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:10.418][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:10.419][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:10.421][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:10.422][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:10.423][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:10.424][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:10.425][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:10.426][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:10.428][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:10.429][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:10.430][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:10.432][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:10.433][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:10.434][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:10.435][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:10.436][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:10.437][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:10.442][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:10.444][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:10.446][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:10.447][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.449][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.463][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[2025-10-04 16:02:10.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.519][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[2025-10-04 16:02:10.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.535][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[2025-10-04 16:02:10.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:10.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:10.548][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:10.556][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:10.558][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.559][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-04 16:02:10.560][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.561][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.562][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.563][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.564][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.565][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-04 16:02:10.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.566][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.567][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-04 16:02:10.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.569][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-04 16:02:10.569][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-04 16:02:10.570][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.571][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.571][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:10.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.574][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.576][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.577][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:10.577][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-04 16:02:10.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.580][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.581][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.582][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-04 16:02:10.583][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.584][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-04 16:02:10.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.588][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.590][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:10.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.592][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-04 16:02:10.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-04 16:02:10.594][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-04 16:02:10.595][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:10.597][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:10.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.602][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:10.602][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:10.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.613][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.614][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.615][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-04 16:02:10.616][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.617][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-04 16:02:10.618][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.619][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.620][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.621][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.622][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.635][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:10.661][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.663][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.667][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-04 16:02:10.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.669][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:10.670][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.671][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:10.671][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:10.671][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:10.672][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:10.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.674][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.678][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:10.678][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:10.678][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:10.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.680][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.681][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:10.682][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-04 16:02:10.683][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.684][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-04 16:02:10.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.686][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:10.687][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.688][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.688][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.689][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.690][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:10.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:10.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.693][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-04 16:02:10.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:10.694][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-04 16:02:10.694][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:10.695][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:10.696][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:10.697][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:10.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.698][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.699][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:10.700][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:10.701][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:10.701][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:10.702][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:10.702][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:10.702][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:10.703][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:10.704][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:10.705][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:10.706][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:10.710][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-04 16:02:10.712][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:10.713][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:10.714][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-04 16:02:10.715][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:10.717][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-04 16:02:10.735][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:10.747][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-10-04 16:02:10.754][biodb::testThat]
biodb.INFO [2025-10-04 16:02:10.755][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:10.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:10.757][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:10.760][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-10-04 16:02:10.761][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:10.764][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-04 16:02:10.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:10.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:10.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:10.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:10.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:10.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:10.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:10.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.809][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:10.827][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.829][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.858][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.864][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:10.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:10.913][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-10-04 16:02:10.955][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.958][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:10.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.979][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:10.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:10.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:10.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:10.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:10.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:10.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.989][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:10.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:10.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:10.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:10.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:10.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:10.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.037][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.043][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.067][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.070][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.081][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.084][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.090][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.091][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.093][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.094][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.105][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.106][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.107][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.112][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.113][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.114][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.128][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-10-04 16:02:11.158][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:11.159][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-10-04 16:02:11.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:11.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:11.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:11.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:11.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.196][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.197][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.199][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.200][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.207][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.214][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:11.245][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-10-04 16:02:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.287][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:11.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:11.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.295][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:11.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:11.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:11.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.353][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:11.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.378][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.381][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.391][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.402][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.405][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.406][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.407][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.408][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-10-04 16:02:11.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.419][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.420][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:11.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.421][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:11.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:11.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:11.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:11.428][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:11.435][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.436][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:11.437][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.438][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:11.439][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-10-04 16:02:11.443][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:11.445][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-04 16:02:11.447][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:11.447][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:11.448][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:11.449][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:11.484][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.485][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:11.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.486][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.492][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.493][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:11.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.494][biodb::testThat]
biodb.WARN [2025-10-04 16:02:11.516][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-04 16:02:11.531][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-04 16:02:11.540][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.541][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:11.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.542][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:11.556][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-10-04 16:02:11.595][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:11.616][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-04 16:02:11.617][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:11.618][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:11.619][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:11.620][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:11.648][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.649][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:11.650][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.651][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.663][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.663][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:11.664][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.665][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.672][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.672][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:11.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.674][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.690][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.691][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:11.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:11.692][biodb::testThat]
biodb.INFO [2025-10-04 16:02:11.698][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:11.699][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-04 16:02:11.700][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:11.700][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:11.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:11.702][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.703][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-04 16:02:11.712][biodb::testContext]
biodb.INFO [2025-10-04 16:02:11.712][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:11.713][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-10-04 16:02:11.714][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:11.715][biodb::testContext]
biodb.INFO [2025-10-04 16:02:11.717][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:11.718][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:11.722][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:11.723][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:11.723][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.726][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:11.727][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.730][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:11.731][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.733][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[2025-10-04 16:02:11.734][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:11.735][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:11.736][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:11.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.739][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:11.740][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:11.741][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.744][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:11.744][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:11.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.748][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:11.748][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:11.749][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:11.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.752][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:11.753][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.756][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:11.757][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:11.758][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:11.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.760][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:11.761][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:11.762][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:11.763][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:11.763][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:11.764][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:11.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.768][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:11.768][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:11.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.771][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:11.772][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:11.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.775][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:11.780][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:11.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.782][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:11.783][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:11.784][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:11.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.787][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:11.788][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:11.805][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:11.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.808][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:11.809][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:11.809][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:11.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.812][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:11.814][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.815][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:02:11.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:11.817][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.820][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:11.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:11.821][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.822][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:11.823][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:11.824][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:11.825][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:11.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:11.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:11.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.831][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:11.833][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:11.834][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.834][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.835][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:11.837][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.837][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:11.838][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:11.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.843][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:11.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:11.844][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.845][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:11.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:11.847][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.849][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:11.849][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:11.849][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:11.849][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:11.849][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:11.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:11.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:11.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.854][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.855][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.855][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:11.856][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:11.857][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.858][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.859][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:11.860][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.861][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:02:11.862][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.863][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:11.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.865][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.865][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.866][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.867][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:11.868][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:11.868][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.869][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:11.870][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:11.871][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.871][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.872][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.873][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:11.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:11.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.878][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.878][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.879][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:11.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:11.880][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.881][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.882][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:11.884][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.885][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:11.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:11.891][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:11.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:11.896][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.897][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:11.898][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:11.899][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.899][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:11.900][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.901][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:11.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:11.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:11.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:11.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:11.906][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:11.908][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:11.909][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:11.909][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:11.910][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:11.911][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.941][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.DEBUG[2025-10-04 16:02:11.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.948][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[2025-10-04 16:02:11.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.968][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[2025-10-04 16:02:11.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:11.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:11.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:11.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:11.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:11.973][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:11.974][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:11.976][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:11.977][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:11.979][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:11.980][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:11.982][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:11.984][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:11.985][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:11.987][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:11.993][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:11.995][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:11.996][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:11.998][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:12.000][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:12.001][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:12.003][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:12.005][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:12.007][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:12.008][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:12.010][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:12.012][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:12.015][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:12.017][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:12.018][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:12.021][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:12.023][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:12.025][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:12.027][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:12.029][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:12.031][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:12.033][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:12.035][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:12.037][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:12.039][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:12.041][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:12.043][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:12.045][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:12.046][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:12.048][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:12.050][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:12.052][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:12.054][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:12.056][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:12.058][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:12.060][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:12.062][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:12.065][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:12.067][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:12.069][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:12.071][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:12.073][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:12.075][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:12.077][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:12.079][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:12.081][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:12.083][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:12.085][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:12.087][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:12.089][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:12.090][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:12.091][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:12.093][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:12.094][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:12.095][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:12.096][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:12.098][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:12.099][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:12.100][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:12.101][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:12.102][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:12.104][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:12.105][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:12.106][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:12.108][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:12.109][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:12.111][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:12.113][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:12.115][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:12.117][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:12.118][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:12.119][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:12.120][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:12.122][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:12.123][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:12.125][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:12.125][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.127][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.236][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[2025-10-04 16:02:12.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.241][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[2025-10-04 16:02:12.243][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:12.245][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:12.246][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.247][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-04 16:02:12.248][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.251][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.251][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.252][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.253][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-04 16:02:12.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.255][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.260][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-04 16:02:12.261][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.261][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-04 16:02:12.261][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-04 16:02:12.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.263][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.264][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:12.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.266][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.268][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.269][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:12.269][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-04 16:02:12.270][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.271][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.272][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.273][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-04 16:02:12.274][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.275][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-04 16:02:12.275][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.278][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.279][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.280][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:12.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.283][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-04 16:02:12.284][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-04 16:02:12.285][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.286][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:12.287][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:12.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.289][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.290][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.291][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.292][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.292][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:12.293][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.294][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.294][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.295][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.296][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-04 16:02:12.298][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.299][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-04 16:02:12.299][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.302][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.303][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.304][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:12.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.306][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-04 16:02:12.307][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.308][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:12.309][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.309][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:12.309][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:12.309][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:12.310][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:12.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.316][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.316][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:12.316][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:12.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.318][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.318][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:12.319][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-04 16:02:12.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.321][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-04 16:02:12.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.323][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.324][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.326][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.327][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:12.328][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.329][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.330][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-04 16:02:12.330][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.331][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-04 16:02:12.331][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:12.332][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.333][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.333][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:12.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.335][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.338][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.338][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:12.338][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:12.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.340][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.341][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:12.345][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-04 16:02:12.350][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:12.351][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:12.352][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-04 16:02:12.353][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:12.354][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-04 16:02:12.361][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-10-04 16:02:12.423][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-10-04 16:02:12.432][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.433][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:12.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.434][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:12.439][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-10-04 16:02:12.440][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:12.442][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-10-04 16:02:12.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:12.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:12.462][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.464][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.477][ef$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:12.478][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:12.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.479][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.480][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-10-04 16:02:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-10-04 16:02:12.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.483][ef$get] Asked field names are: location.
biodb.TRACE[2025-10-04 16:02:12.484][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-04 16:02:12.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.486][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.487][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-10-04 16:02:12.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-10-04 16:02:12.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.490][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-10-04 16:02:12.491][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-04 16:02:12.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.492][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.494][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-10-04 16:02:12.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-10-04 16:02:12.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.497][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-04 16:02:12.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:12.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.499][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.501][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-10-04 16:02:12.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:12.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.504][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-04 16:02:12.505][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-04 16:02:12.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.506][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.509][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-10-04 16:02:12.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-10-04 16:02:12.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-10-04 16:02:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:12.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:12.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:12.556][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-10-04 16:02:12.557][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:12.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:12.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.561][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:12.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:12.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:12.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:12.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:12.574][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-10-04 16:02:12.596][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:12.611][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-10-04 16:02:12.612][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-10-04 16:02:12.615][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:12.616][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-10-04 16:02:12.617][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:12.617][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:12.618][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:12.619][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:12.630][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.631][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:12.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.632][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:12.634][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-10-04 16:02:12.635][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-10-04 16:02:12.636][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-04 16:02:12.637][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:12.638][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.639][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:12.640][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:12.641][private$retrieveContents] Get entry content(s) for 8 id(s)...
biodb.INFO [2025-10-04 16:02:12.655][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.656][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:12.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.658][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:12.660][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:12.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:12.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:12.663][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:12.664][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-10-04 16:02:12.672][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-04 16:02:12.673][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:12.674][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-04 16:02:12.675][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:12.676][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.676][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:12.677][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:12.694][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:12.718][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.719][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:12.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.721][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:12.727][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-04 16:02:12.728][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:12.729][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-04 16:02:12.730][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:12.731][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.732][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:12.733][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:12.733][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:12.746][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.747][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:12.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.748][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:12.751][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-10-04 16:02:12.752][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:12.753][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-10-04 16:02:12.754][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:12.755][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:12.755][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:12.756][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:12.757][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:12.774][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.775][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:12.776][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.776][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.788][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.788][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:12.789][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.790][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.796][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.797][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:12.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.798][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.810][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.811][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:12.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:12.812][biodb::testThat]
biodb.INFO [2025-10-04 16:02:12.818][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:12.819][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-10-04 16:02:12.820][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-10-04 16:02:12.820][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:12.821][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:12.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:12.822][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:12.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:12.824][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-04 16:02:12.827][biodb::testContext]
biodb.INFO [2025-10-04 16:02:12.828][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:12.829][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-10-04 16:02:12.830][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:12.831][biodb::testContext]
biodb.INFO [2025-10-04 16:02:12.832][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:12.834][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:12.837][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:12.838][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:12.839][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.842][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:12.843][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.846][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:12.846][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.849][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:12.850][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:12.851][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:12.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.854][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:12.855][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:12.856][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.863][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:12.864][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:12.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.867][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:12.868][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:12.869][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:12.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.871][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:12.872][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.875][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:12.876][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:12.877][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:12.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.880][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:12.881][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:12.882][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:12.882][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:12.883][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:12.884][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:12.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.886][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:12.887][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:12.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.890][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:12.891][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:12.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.894][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:12.894][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:12.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.898][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:12.898][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:12.899][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:12.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.902][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:12.903][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:12.921][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:12.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.924][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:12.925][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:12.926][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:12.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:12.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:12.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:12.929][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:12.931][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.932][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:02:12.932][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.933][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.934][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.935][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.936][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.937][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:12.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.939][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.940][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:12.940][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.941][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:12.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:12.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:12.943][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:12.943][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:12.944][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:12.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.949][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.951][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.952][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.953][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:12.954][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.955][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:12.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.964][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:12.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.965][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.966][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:12.967][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.968][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:12.969][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:12.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:12.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.976][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:12.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:12.978][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.979][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.980][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:12.981][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.982][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:02:12.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:12.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.985][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.986][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.987][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.987][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:12.988][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:12.989][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:12.990][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:12.991][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:12.992][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:12.993][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:12.994][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:12.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.996][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:12.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:12.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:12.998][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:12.999][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.000][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.002][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.003][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:13.004][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.005][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:13.006][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.007][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:13.008][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.009][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.011][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:13.012][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:13.012][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.013][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:13.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:13.015][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.016][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.017][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:13.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:13.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.022][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.022][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.025][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.026][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:13.027][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.103][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:13.105][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:13.106][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:13.107][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:13.108][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:13.109][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:13.110][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:13.111][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:13.112][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:13.113][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:13.115][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:13.116][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:13.117][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:13.118][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:13.119][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:13.120][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:13.121][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:13.123][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:13.124][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:13.125][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:13.126][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:13.127][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:13.128][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:13.129][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:13.130][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:13.131][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:13.133][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:13.134][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:13.135][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:13.136][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:13.137][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:13.142][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:13.143][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:13.145][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:13.146][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:13.147][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:13.148][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:13.149][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:13.150][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:13.151][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:13.152][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:13.153][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:13.154][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:13.155][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:13.156][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:13.157][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:13.159][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:13.160][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:13.161][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:13.162][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:13.163][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:13.164][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:13.165][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:13.166][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:13.167][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:13.168][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:13.169][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:13.171][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:13.172][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:13.173][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:13.174][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:13.175][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:13.176][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:13.177][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:13.178][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:13.180][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:13.181][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:13.182][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:13.183][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:13.184][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:13.185][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:13.186][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:13.187][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:13.188][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:13.189][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:13.190][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:13.191][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:13.192][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:13.193][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:13.194][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:13.196][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:13.197][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:13.198][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:13.199][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:13.200][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:13.201][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:13.202][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:13.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:13.290][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:13.291][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:13.293][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.294][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-04 16:02:13.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:13.296][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.298][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.300][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-04 16:02:13.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:13.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.302][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-04 16:02:13.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:13.304][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-04 16:02:13.304][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-04 16:02:13.305][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.310][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.311][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:13.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:13.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.315][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.316][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:13.316][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-04 16:02:13.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.318][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.319][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.319][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.320][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-04 16:02:13.322][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.323][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-04 16:02:13.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:13.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.327][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.328][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.329][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:13.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:13.330][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.331][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-04 16:02:13.332][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-04 16:02:13.333][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.334][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:13.335][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:13.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.337][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:13.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.339][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.340][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:13.340][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:13.340][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.341][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.342][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.342][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.343][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-04 16:02:13.345][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.346][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-04 16:02:13.346][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.347][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:13.348][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.349][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.351][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:13.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:13.352][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.353][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.354][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:13.355][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:13.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:13.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:13.357][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:13.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.359][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:13.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.361][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.362][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:13.362][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:13.362][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:13.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.364][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.365][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:13.366][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-04 16:02:13.367][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.368][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-04 16:02:13.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:13.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.371][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.373][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:13.374][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:13.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.375][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-04 16:02:13.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:13.376][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-04 16:02:13.376][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:13.377][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:13.378][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:13.379][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:13.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:13.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:13.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:13.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:13.384][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:13.384][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:13.384][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:13.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:13.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:13.390][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:13.391][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:13.396][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-04 16:02:13.397][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:13.398][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:13.399][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-04 16:02:13.400][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:13.401][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-04 16:02:13.407][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-04 16:02:13.413][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-10-04 16:02:13.417][biodb::testThat]
biodb.INFO [2025-10-04 16:02:13.417][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:13.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:13.419][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:13.421][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-10-04 16:02:13.423][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:13.425][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-04 16:02:13.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:13.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:13.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:13.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:13.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:13.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:13.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:13.438][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.440][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.441][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.454][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.455][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.456][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.461][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.462][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.463][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.464][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.468][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.468][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.470][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.480][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.481][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.482][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.487][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.488][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.489][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.494][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:13.495][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.496][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.497][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.500][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.501][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.502][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.507][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:13.508][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:13.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.509][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:13.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:13.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.513][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:13.514][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:13.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.516][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:13.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:13.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.520][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.521][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.522][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.524][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.527][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:13.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.529][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.534][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.534][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.536][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.540][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.541][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.543][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.547][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-04 16:02:13.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-04 16:02:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-04 16:02:13.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.580][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-04 16:02:13.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.587][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-04 16:02:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.597][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:13.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:13.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.607][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:13.635][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-10-04 16:02:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:13.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:13.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:13.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:13.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.653][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:13.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:13.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:13.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:13.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.671][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.699][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.701][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:13.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.727][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.730][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.750][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:13.751][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.752][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:13.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.773][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:13.774][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.776][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.796][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.797][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.799][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.814][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.817][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.823][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.824][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.825][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.826][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:13.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.845][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.846][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.848][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.848][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.862][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.869][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.869][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.871][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:13.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.897][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.897][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.899][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:13.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.913][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.920][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.921][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.922][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:13.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.940][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.943][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.944][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.945][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:13.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.956][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.966][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.967][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.968][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.984][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.987][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.994][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.995][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:13.996][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:13.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.018][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.019][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.021][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.043][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.044][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.045][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.073][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.075][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.086][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.089][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.094][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.095][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.096][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.100][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.101][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.103][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.108][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.108][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.110][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.114][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.115][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.117][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.121][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.122][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.123][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.127][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.129][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.134][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.135][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.136][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.141][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.142][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.143][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.147][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.148][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.154][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.159][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.160][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.161][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.166][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.167][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.168][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.173][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.174][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.176][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.180][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.181][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.182][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.187][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.188][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.189][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.194][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-10-04 16:02:14.195][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:14.196][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-10-04 16:02:14.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:14.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:14.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:14.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:14.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:14.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:14.208][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.210][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.214][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.215][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.217][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.221][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.222][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.224][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.225][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.228][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.229][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.231][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.235][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.236][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.237][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.243][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.246][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.247][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.249][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.253][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:14.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.255][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.256][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.257][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-10-04 16:02:14.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.260][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.261][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.263][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.264][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.267][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.268][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.269][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.275][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.276][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.281][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.282][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.283][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.284][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.288][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:14.289][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.290][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-10-04 16:02:14.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.294][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.295][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.297][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.301][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.302][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.303][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.308][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-10-04 16:02:14.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-10-04 16:02:14.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.333][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-10-04 16:02:14.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.343][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-10-04 16:02:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.346][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.350][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-10-04 16:02:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.370][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.377][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:14.400][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-10-04 16:02:14.401][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:14.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:14.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:14.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:14.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:14.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:14.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:14.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:14.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:14.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:14.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.424][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:14.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:14.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.436][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.495][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.496][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.496][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.497][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.518][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.519][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.521][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.542][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.542][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.544][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.564][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.565][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.567][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.587][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.593][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.594][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.596][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.597][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.618][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.619][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.621][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.636][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.642][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.643][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.645][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.671][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.672][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.674][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.696][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.697][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.698][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.713][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.720][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.721][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.722][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.723][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.744][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.744][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.746][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.751][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.762][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.773][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.774][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.775][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.795][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.798][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.799][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.801][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.822][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.823][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.825][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.857][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.858][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.859][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.871][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:14.872][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:14.873][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.874][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.879][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.879][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-10-04 16:02:14.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.881][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.886][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.887][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-10-04 16:02:14.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.888][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.893][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.894][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-10-04 16:02:14.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.896][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.900][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.901][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-10-04 16:02:14.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.903][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.908][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.908][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-10-04 16:02:14.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.910][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.914][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-04 16:02:14.915][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-04 16:02:14.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.917][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.921][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-04 16:02:14.922][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-04 16:02:14.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.924][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.928][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.929][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-04 16:02:14.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.931][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.940][ef$get] Asked field names are: logp.
biodb.TRACE[2025-10-04 16:02:14.941][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-10-04 16:02:14.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.943][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.948][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.949][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:14.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.950][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.955][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-10-04 16:02:14.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.957][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.962][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:14.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:14.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.965][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.969][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.970][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-10-04 16:02:14.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.971][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:14.976][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.977][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-10-04 16:02:14.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:14.978][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:14.986][biodb::testThat]
biodb.INFO [2025-10-04 16:02:14.987][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:14.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:14.988][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:14.990][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:14.993][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:14.994][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:14.995][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:14.996][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:14.997][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:14.998][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:14.999][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-04 16:02:15.010][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.011][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:15.012][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.013][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:15.015][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:15.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:15.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.017][ef$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:15.018][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-10-04 16:02:15.027][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-04 16:02:15.028][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:15.029][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.034][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.035][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.036][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.037][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.038][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:15.049][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.050][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:15.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.052][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.059][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-04 16:02:15.059][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:15.061][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.061][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.062][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.065][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:15.077][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.078][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:15.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.079][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.083][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-04 16:02:15.084][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:15.085][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.086][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.087][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.087][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.088][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.089][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:15.101][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.102][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:15.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.103][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.119][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.120][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:15.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.122][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.134][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.135][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:15.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.137][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.148][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.149][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:15.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.151][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:15.169][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:15.170][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:15.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.172][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.173][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:15.174][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:15.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.175][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:15.176][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.177][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-10-04 16:02:15.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.178][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.185][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-10-04 16:02:15.186][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:15.187][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.188][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.189][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.190][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.190][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.191][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:15.208][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.209][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-10-04 16:02:15.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.211][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.213][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:15.214][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:15.216][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.217][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.217][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.218][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.219][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.220][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-04 16:02:15.232][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.233][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-10-04 16:02:15.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.235][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.238][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:15.238][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:15.240][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.240][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.241][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.242][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.243][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.243][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-04 16:02:15.255][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.256][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-10-04 16:02:15.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.257][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.259][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:15.260][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:15.261][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.262][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.263][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.264][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.265][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.265][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.TRACE[2025-10-04 16:02:15.282][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-04 16:02:15.283][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-04 16:02:15.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.285][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.286][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:15.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-04 16:02:15.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.288][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:15.289][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.290][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-10-04 16:02:15.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.292][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.294][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:15.295][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:15.297][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.298][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.298][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.299][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.300][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.301][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-04 16:02:15.313][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.314][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-10-04 16:02:15.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.315][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:15.318][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-10-04 16:02:15.318][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-10-04 16:02:15.319][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:15.320][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:15.321][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.322][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:15.323][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:15.324][private$retrieveContents] Get entry content(s) for 2 id(s)...
biodb.INFO [2025-10-04 16:02:15.335][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:15.336][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-10-04 16:02:15.337][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:15.338][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.339][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.340][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-04 16:02:15.344][biodb::testContext]
biodb.INFO [2025-10-04 16:02:15.345][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:15.346][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-10-04 16:02:15.347][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-04 16:02:15.347][biodb::testContext]
biodb.INFO [2025-10-04 16:02:15.349][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:15.350][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:15.353][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:15.354][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-04 16:02:15.355][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.358][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-04 16:02:15.359][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.367][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-04 16:02:15.368][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.371][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-04 16:02:15.372][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-04 16:02:15.373][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-04 16:02:15.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.376][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-04 16:02:15.377][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-04 16:02:15.378][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.381][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-04 16:02:15.382][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-04 16:02:15.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.385][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-04 16:02:15.386][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-04 16:02:15.386][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-04 16:02:15.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.389][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-04 16:02:15.390][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.393][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-04 16:02:15.394][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-04 16:02:15.395][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-04 16:02:15.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.398][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:15.399][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-04 16:02:15.400][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-04 16:02:15.401][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-04 16:02:15.402][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-04 16:02:15.402][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-04 16:02:15.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.405][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-04 16:02:15.406][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-04 16:02:15.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.409][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-04 16:02:15.410][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-04 16:02:15.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.413][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-04 16:02:15.414][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-04 16:02:15.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.417][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-04 16:02:15.418][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-04 16:02:15.419][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-04 16:02:15.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.422][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-04 16:02:15.423][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-04 16:02:15.441][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-04 16:02:15.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.444][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-04 16:02:15.445][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-04 16:02:15.446][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-04 16:02:15.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.449][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-04 16:02:15.450][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.451][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-04 16:02:15.452][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.453][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.454][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.455][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.456][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.457][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:15.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.463][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.464][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-04 16:02:15.465][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.466][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:15.467][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:15.468][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:15.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.471][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.474][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.476][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.477][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.478][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-04 16:02:15.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.480][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:15.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.485][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.486][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.486][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:15.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.489][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-04 16:02:15.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.491][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.491][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.492][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:15.492][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:15.492][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:15.492][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-04 16:02:15.492][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-04 16:02:15.493][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:15.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.499][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.500][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.500][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.501][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.502][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.503][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-04 16:02:15.505][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.505][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-04 16:02:15.506][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.507][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.508][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.509][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-04 16:02:15.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.513][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.514][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-04 16:02:15.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.516][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.517][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:15.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.524][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.524][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.525][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.526][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.526][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.527][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-04 16:02:15.529][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.530][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-04 16:02:15.531][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.536][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-04 16:02:15.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.542][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.543][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-04 16:02:15.544][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.545][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.546][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.547][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-04 16:02:15.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.553][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.554][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.555][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.555][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.557][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:15.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.558][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[2025-10-04 16:02:15.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.566][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[2025-10-04 16:02:15.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.623][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-04 16:02:15.625][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-04 16:02:15.626][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-04 16:02:15.627][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-04 16:02:15.628][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-04 16:02:15.629][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-04 16:02:15.631][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:15.632][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:15.633][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-04 16:02:15.634][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-04 16:02:15.635][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-04 16:02:15.636][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-04 16:02:15.638][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-04 16:02:15.639][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-04 16:02:15.640][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:15.641][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:15.642][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-04 16:02:15.643][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-04 16:02:15.644][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-04 16:02:15.645][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-04 16:02:15.647][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-04 16:02:15.648][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-04 16:02:15.649][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-04 16:02:15.650][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-04 16:02:15.651][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-04 16:02:15.652][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-04 16:02:15.653][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-04 16:02:15.654][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-04 16:02:15.655][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-04 16:02:15.657][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-04 16:02:15.658][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-04 16:02:15.659][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-04 16:02:15.660][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-04 16:02:15.661][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-04 16:02:15.662][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-04 16:02:15.663][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-04 16:02:15.664][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-04 16:02:15.665][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-04 16:02:15.666][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-04 16:02:15.668][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-04 16:02:15.669][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-04 16:02:15.670][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-04 16:02:15.671][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-04 16:02:15.672][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-04 16:02:15.673][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-04 16:02:15.674][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:15.676][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-04 16:02:15.677][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-04 16:02:15.678][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-04 16:02:15.679][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-04 16:02:15.680][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-04 16:02:15.681][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-04 16:02:15.682][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-04 16:02:15.683][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-04 16:02:15.684][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-04 16:02:15.685][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-04 16:02:15.686][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-04 16:02:15.687][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-04 16:02:15.689][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-04 16:02:15.690][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-04 16:02:15.695][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-04 16:02:15.696][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-04 16:02:15.698][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-04 16:02:15.699][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-04 16:02:15.700][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-04 16:02:15.701][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-04 16:02:15.702][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-04 16:02:15.703][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-04 16:02:15.704][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-04 16:02:15.705][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-04 16:02:15.707][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-04 16:02:15.708][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-04 16:02:15.709][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-04 16:02:15.710][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-04 16:02:15.711][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-04 16:02:15.712][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-04 16:02:15.713][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-04 16:02:15.714][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-04 16:02:15.715][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-04 16:02:15.716][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-04 16:02:15.717][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-04 16:02:15.719][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-04 16:02:15.720][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-04 16:02:15.721][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-04 16:02:15.722][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-04 16:02:15.723][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-04 16:02:15.724][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.726][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.741][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[2025-10-04 16:02:15.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.756][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[2025-10-04 16:02:15.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-04 16:02:15.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-04 16:02:15.811][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-10-04 16:02:15.813][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-10-04 16:02:15.814][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.815][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-10-04 16:02:15.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.818][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.819][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.821][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-10-04 16:02:15.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.822][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.823][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-10-04 16:02:15.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.825][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-10-04 16:02:15.825][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-10-04 16:02:15.826][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.826][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.827][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:15.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.832][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-10-04 16:02:15.832][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-10-04 16:02:15.833][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.835][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.835][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.836][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-10-04 16:02:15.838][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.843][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-10-04 16:02:15.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.845][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.846][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.847][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.849][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:15.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.850][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.851][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-10-04 16:02:15.852][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-10-04 16:02:15.853][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:15.855][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-04 16:02:15.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.861][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.861][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:15.861][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.863][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.864][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.865][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-10-04 16:02:15.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.867][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-10-04 16:02:15.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.872][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.872][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.873][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:15.874][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.875][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.876][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-10-04 16:02:15.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.878][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-10-04 16:02:15.879][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.880][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-04 16:02:15.880][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-04 16:02:15.880][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-04 16:02:15.880][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:15.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.886][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.886][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:15.886][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:15.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.889][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.890][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:15.891][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-04 16:02:15.892][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.893][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-10-04 16:02:15.894][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-04 16:02:15.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.897][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.898][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.899][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-10-04 16:02:15.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-04 16:02:15.900][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.901][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-10-04 16:02:15.902][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-04 16:02:15.903][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-10-04 16:02:15.903][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-10-04 16:02:15.903][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-04 16:02:15.904][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-04 16:02:15.905][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-10-04 16:02:15.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-04 16:02:15.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-04 16:02:15.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-04 16:02:15.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-04 16:02:15.910][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:15.910][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-10-04 16:02:15.910][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-10-04 16:02:15.910][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-04 16:02:15.911][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-04 16:02:15.912][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-04 16:02:15.913][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-10-04 16:02:15.922][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-10-04 16:02:15.923][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-04 16:02:15.924][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-04 16:02:15.925][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-10-04 16:02:15.926][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-04 16:02:15.927][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-10-04 16:02:15.931][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-10-04 16:02:15.938][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-10-04 16:02:15.942][biodb::testThat]
biodb.INFO [2025-10-04 16:02:15.942][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-04 16:02:15.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:15.944][biodb::testThat]
biodb.TRACE[2025-10-04 16:02:15.946][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-10-04 16:02:15.947][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-10-04 16:02:15.950][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-10-04 16:02:15.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-04 16:02:15.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:15.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:15.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:15.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:15.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:15.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-04 16:02:15.962][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:15.963][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:15.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.964][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:15.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:15.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.979][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:15.979][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:15.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.981][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.982][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:15.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:15.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:15.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-04 16:02:16.023][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-10-04 16:02:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-10-04 16:02:16.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-10-04 16:02:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.031][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:16.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-10-04 16:02:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.034][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:16.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.037][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-04 16:02:16.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-04 16:02:16.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:16.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-04 16:02:16.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.043][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:16.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-04 16:02:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-10-04 16:02:16.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.238][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.240][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.257][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.260][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.261][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.263][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.264][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.274][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-04 16:02:16.275][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-04 16:02:16.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.276][ef$get] fields variable is a list.
biodb.TRACE[2025-10-04 16:02:16.280][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.281][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-10-04 16:02:16.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-04 16:02:16.283][ef$get] fields variable is a list.
biodb.INFO [2025-10-04 16:02:16.290][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.290][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-04 16:02:16.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.292][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:16.294][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-04 16:02:16.297][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:16.298][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:16.299][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:16.300][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:16.301][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:16.302][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:16.303][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:16.315][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.316][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-04 16:02:16.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.318][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.324][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.325][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-04 16:02:16.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.327][biodb::testThat]
biodb.WARN [2025-10-04 16:02:16.330][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-04 16:02:16.333][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-04 16:02:16.342][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.343][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-04 16:02:16.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.344][biodb::testThat]
biodb.DEBUG[2025-10-04 16:02:16.348][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-10-04 16:02:16.349][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-10-04 16:02:16.350][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-10-04 16:02:16.351][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-10-04 16:02:16.352][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-10-04 16:02:16.353][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-10-04 16:02:16.354][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-10-04 16:02:16.355][private$retrieveContents] Get entry content(s) for 1 id(s)...
biodb.INFO [2025-10-04 16:02:16.368][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.369][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-04 16:02:16.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.370][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.384][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.385][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-04 16:02:16.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.387][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.401][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.402][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:16.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.404][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.417][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.418][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-04 16:02:16.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-04 16:02:16.420][biodb::testThat]
biodb.INFO [2025-10-04 16:02:16.433][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-04 16:02:16.434][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-10-04 16:02:16.435][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-04 16:02:16.436][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-04 16:02:16.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-04 16:02:16.438][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-04 16:02:16.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-04 16:02:16.439][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-04 16:02:16.440][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".
[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$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$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$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$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$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$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, 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$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
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 biodbNcbi_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
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 files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... WARNING
'library' or 'require' call not declared from: ‘biodbNci’
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 0 | PASS 247 ]
  Error: Test failures
  In addition: Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.13.1’
** using staged installation
** 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 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)