Back to Long Tests report for BioC 3.22

This page was generated on 2025-10-25 23:55 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-10-25 09:55 -0400 (Sat, 25 Oct 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-10-25 16:01:21 -0400 (Sat, 25 Oct 2025)
EndedAt: 2025-10-25 16:02:20 -0400 (Sat, 25 Oct 2025)
EllapsedTime: 59.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-10-25 16:02:17.427][biodb::testContext]
biodb.INFO [2025-10-25 16:02:17.430][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:17.431][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-10-25 16:02:17.432][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:17.432][biodb::testContext]
biodb.INFO [2025-10-25 16:02:17.437][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:17.439][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:17.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:17.445][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-25 16:02:17.446][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.449][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-25 16:02:17.463][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.466][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-25 16:02:17.467][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.478][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-25 16:02:17.479][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-25 16:02:17.480][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-25 16:02:17.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.482][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-25 16:02:17.483][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-25 16:02:17.484][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.487][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-25 16:02:17.487][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-25 16:02:17.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.489][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[2025-10-25 16:02:17.490][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-25 16:02:17.491][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-25 16:02:17.491][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-25 16:02:17.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.494][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-25 16:02:17.495][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.497][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-25 16:02:17.498][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-25 16:02:17.499][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-25 16:02:17.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.502][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:17.502][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-25 16:02:17.503][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-25 16:02:17.504][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-25 16:02:17.505][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-25 16:02:17.505][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-25 16:02:17.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.508][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-25 16:02:17.509][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-25 16:02:17.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.512][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-25 16:02:17.513][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-25 16:02:17.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.515][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-25 16:02:17.516][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-25 16:02:17.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.519][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-25 16:02:17.519][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-25 16:02:17.520][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-25 16:02:17.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.523][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:17.524][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-25 16:02:17.541][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-25 16:02:17.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.544][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-25 16:02:17.545][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-25 16:02:17.546][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-25 16:02:17.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.550][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-25 16:02:17.575][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.587][self$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[2025-10-25 16:02:17.589][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:17.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.592][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.593][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:17.594][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:17.594][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.595][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-25 16:02:17.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:17.597][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:17.598][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:17.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:17.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:17.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.604][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:17.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:17.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.607][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.608][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-25 16:02:17.610][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.611][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:17.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:17.617][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.619][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.620][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:17.621][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:17.622][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.623][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-25 16:02:17.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:17.624][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.625][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.626][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:17.626][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:17.626][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:17.626][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:17.626][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:17.627][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:17.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:17.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.632][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:17.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:17.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.635][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.636][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-25 16:02:17.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.638][self$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[2025-10-25 16:02:17.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:17.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.644][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:17.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:17.645][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.646][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-25 16:02:17.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:17.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.650][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.650][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:17.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.653][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:17.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.656][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:17.657][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:17.658][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.659][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.660][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-25 16:02:17.661][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.662][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:17.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:17.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.666][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.668][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:17.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:17.670][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.670][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-25 16:02:17.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:17.672][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.673][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:17.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.676][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:17.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.679][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:17.681][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:17.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.682][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:17.686][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.704][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.DEBUG[2025-10-25 16:02:17.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.729][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[2025-10-25 16:02:17.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.736][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[2025-10-25 16:02:17.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.743][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[2025-10-25 16:02:17.744][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-25 16:02:17.751][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-25 16:02:17.752][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-25 16:02:17.753][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-25 16:02:17.754][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-25 16:02:17.755][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:02:17.756][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:17.758][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:17.759][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-25 16:02:17.760][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:02:17.761][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:02:17.762][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-25 16:02:17.763][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:17.764][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:17.765][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-25 16:02:17.766][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:02:17.767][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-25 16:02:17.768][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-25 16:02:17.769][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-25 16:02:17.770][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-25 16:02:17.772][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-25 16:02:17.773][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-25 16:02:17.774][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-25 16:02:17.775][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-25 16:02:17.776][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-25 16:02:17.777][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-25 16:02:17.778][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-25 16:02:17.779][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-25 16:02:17.780][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-25 16:02:17.781][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-25 16:02:17.782][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-25 16:02:17.783][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-25 16:02:17.784][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-25 16:02:17.785][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-25 16:02:17.786][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-25 16:02:17.788][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-25 16:02:17.789][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-25 16:02:17.790][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-25 16:02:17.791][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-25 16:02:17.792][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-25 16:02:17.793][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-25 16:02:17.795][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-25 16:02:17.796][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-25 16:02:17.797][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-25 16:02:17.798][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-25 16:02:17.799][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-25 16:02:17.800][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-25 16:02:17.802][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-25 16:02:17.803][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-25 16:02:17.804][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-25 16:02:17.806][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-25 16:02:17.808][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-25 16:02:17.810][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-25 16:02:17.812][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-25 16:02:17.815][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-25 16:02:17.817][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-25 16:02:17.819][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-25 16:02:17.820][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-25 16:02:17.822][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-25 16:02:17.823][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-25 16:02:17.824][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-25 16:02:17.825][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-25 16:02:17.826][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-25 16:02:17.827][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-25 16:02:17.828][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-25 16:02:17.830][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-25 16:02:17.831][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-25 16:02:17.832][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-25 16:02:17.834][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-25 16:02:17.835][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-25 16:02:17.836][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-25 16:02:17.838][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-25 16:02:17.839][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-25 16:02:17.841][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-25 16:02:17.842][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-25 16:02:17.843][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-25 16:02:17.844][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-25 16:02:17.845][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-25 16:02:17.846][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-25 16:02:17.847][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-25 16:02:17.849][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-25 16:02:17.850][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-25 16:02:17.851][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-25 16:02:17.856][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-25 16:02:17.859][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:17.863][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:17.864][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.866][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.886][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[2025-10-25 16:02:17.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.928][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[2025-10-25 16:02:17.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.937][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[2025-10-25 16:02:17.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:17.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:17.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:17.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:17.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:17.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:17.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:17.953][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:17.960][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-25 16:02:17.962][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.963][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-25 16:02:17.963][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:17.965][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.966][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-25 16:02:17.966][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.967][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.968][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-25 16:02:17.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:17.969][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.970][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-25 16:02:17.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-25 16:02:17.972][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:17.973][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.974][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-25 16:02:17.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:17.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:17.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:17.978][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:17.979][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:02:17.979][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:02:17.979][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-25 16:02:17.979][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-25 16:02:17.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:17.981][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:17.981][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:17.982][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:17.987][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-25 16:02:18.005][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-25 16:02:18.018][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-25 16:02:18.032][biodb::testThat]
biodb.INFO [2025-10-25 16:02:18.033][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-10-25 16:02:18.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:18.034][biodb::testThat]
biodb.TRACE[2025-10-25 16:02:18.036][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-10-25 16:02:18.038][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-25 16:02:18.040][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-25 16:02:18.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-25 16:02:18.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:18.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:18.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:18.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:18.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:18.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-25 16:02:18.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.136][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.151][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:02:18.196][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-10-25 16:02:18.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:18.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:18.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:18.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.225][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.317][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.319][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.339][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.340][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.342][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.343][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.362][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.363][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.364][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.390][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.410][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.410][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.412][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.423][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.424][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.425][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.429][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.430][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.432][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.436][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.438][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.442][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.445][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.449][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.450][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.451][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.466][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-10-25 16:02:18.499][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-10-25 16:02:18.500][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-10-25 16:02:18.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-10-25 16:02:18.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:18.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:18.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:18.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:18.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:18.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-10-25 16:02:18.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.543][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.547][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.625][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.629][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-10-25 16:02:18.660][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-10-25 16:02:18.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.680][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-10-25 16:02:18.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:18.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-10-25 16:02:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:18.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-10-25 16:02:18.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.697][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.735][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-10-25 16:02:18.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.762][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.764][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.775][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.778][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.784][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.785][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.787][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.787][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.806][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.808][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.829][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.832][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.833][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.834][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.855][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.858][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.879][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.880][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.881][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.902][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.903][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.904][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.915][ef$get] Asked field names are: accession.
biodb.TRACE[2025-10-25 16:02:18.916][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-10-25 16:02:18.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.918][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.926][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.927][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-10-25 16:02:18.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.929][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.933][ef$get] Asked field names are: formula.
biodb.TRACE[2025-10-25 16:02:18.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-10-25 16:02:18.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.935][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.940][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-10-25 16:02:18.941][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-10-25 16:02:18.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.942][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.947][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-10-25 16:02:18.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.949][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.953][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-10-25 16:02:18.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.955][ef$get] fields variable is a list.
biodb.TRACE[2025-10-25 16:02:18.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-10-25 16:02:18.960][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-10-25 16:02:18.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-10-25 16:02:18.962][ef$get] fields variable is a list.
biodb.INFO [2025-10-25 16:02:18.969][biodb::testThat]
biodb.INFO [2025-10-25 16:02:18.970][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-10-25 16:02:18.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:18.971][biodb::testThat]
biodb.DEBUG[2025-10-25 16:02:18.973][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-10-25 16:02:18.976][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-10-25 16:02:18.978][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:19.001][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-25 16:02:19.002][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-25 16:02:19.003][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-25 16:02:19.041][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.042][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-10-25 16:02:19.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.043][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.049][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.050][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-10-25 16:02:19.050][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.051][biodb::testThat]
biodb.WARN [2025-10-25 16:02:19.066][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-10-25 16:02:19.080][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-10-25 16:02:19.088][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.089][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-10-25 16:02:19.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.090][biodb::testThat]
biodb.DEBUG[2025-10-25 16:02:19.104][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-10-25 16:02:19.143][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-10-25 16:02:19.144][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-10-25 16:02:19.145][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-10-25 16:02:19.146][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-10-25 16:02:19.156][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-10-25 16:02:19.177][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.178][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-10-25 16:02:19.178][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.179][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.186][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.187][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-10-25 16:02:19.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.188][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.195][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.196][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-10-25 16:02:19.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.198][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.204][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.209][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-10-25 16:02:19.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-10-25 16:02:19.211][biodb::testThat]
biodb.INFO [2025-10-25 16:02:19.217][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-25 16:02:19.218][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-25 16:02:19.219][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-25 16:02:19.219][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.221][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.222][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-10-25 16:02:19.231][biodb::testContext]
biodb.INFO [2025-10-25 16:02:19.231][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:19.232][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-10-25 16:02:19.233][biodb::testContext] ********************************************************************************
biodb.INFO [2025-10-25 16:02:19.234][biodb::testContext]
biodb.INFO [2025-10-25 16:02:19.236][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:19.237][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:19.240][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:19.241][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-10-25 16:02:19.242][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.245][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-10-25 16:02:19.246][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.249][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-10-25 16:02:19.250][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.253][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-10-25 16:02:19.254][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-10-25 16:02:19.254][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-10-25 16:02:19.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.258][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-10-25 16:02:19.258][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-10-25 16:02:19.259][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.262][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-10-25 16:02:19.263][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-10-25 16:02:19.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.266][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-10-25 16:02:19.267][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-10-25 16:02:19.268][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-10-25 16:02:19.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.271][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-10-25 16:02:19.271][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.274][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-10-25 16:02:19.275][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-10-25 16:02:19.275][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-10-25 16:02:19.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.278][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:19.279][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-10-25 16:02:19.280][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-10-25 16:02:19.280][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-10-25 16:02:19.281][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-10-25 16:02:19.282][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-10-25 16:02:19.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.285][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-10-25 16:02:19.285][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-10-25 16:02:19.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.288][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-10-25 16:02:19.289][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-10-25 16:02:19.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.291][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-10-25 16:02:19.292][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-10-25 16:02:19.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.294][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[2025-10-25 16:02:19.295][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-10-25 16:02:19.296][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-10-25 16:02:19.297][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-10-25 16:02:19.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.300][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-10-25 16:02:19.301][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-10-25 16:02:19.318][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-10-25 16:02:19.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.325][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-10-25 16:02:19.326][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-10-25 16:02:19.327][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-10-25 16:02:19.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.330][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-10-25 16:02:19.331][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.332][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-10-25 16:02:19.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:19.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.335][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.337][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:19.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:19.338][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.339][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-10-25 16:02:19.340][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:19.341][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.342][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:19.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:19.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:19.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.349][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:19.350][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:19.351][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.352][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.353][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-10-25 16:02:19.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.355][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:19.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.356][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:19.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.359][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.359][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.360][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:19.361][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:19.362][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.362][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-10-25 16:02:19.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:19.364][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-10-25 16:02:19.365][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-10-25 16:02:19.366][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:19.367][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.367][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.368][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:19.369][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.370][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.371][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.372][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:19.373][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:19.373][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.374][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.375][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-10-25 16:02:19.377][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.377][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-10-25 16:02:19.378][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:19.380][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-10-25 16:02:19.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:19.385][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.385][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-10-25 16:02:19.386][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:19.387][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.388][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.389][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.390][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:19.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:19.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.394][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.395][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:19.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:19.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.398][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.399][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-10-25 16:02:19.400][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.401][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-10-25 16:02:19.402][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:19.404][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.405][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.407][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-10-25 16:02:19.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:19.409][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.410][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-10-25 16:02:19.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:19.412][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.412][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.413][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-10-25 16:02:19.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:19.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.456][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:19.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:19.458][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.459][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:19.461][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.512][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[2025-10-25 16:02:19.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.520][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-10-25 16:02:19.521][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-10-25 16:02:19.522][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-10-25 16:02:19.523][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-10-25 16:02:19.524][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-10-25 16:02:19.525][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-10-25 16:02:19.526][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:19.527][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:19.528][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-10-25 16:02:19.529][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-10-25 16:02:19.530][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-10-25 16:02:19.531][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-10-25 16:02:19.532][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-10-25 16:02:19.533][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-10-25 16:02:19.534][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-10-25 16:02:19.535][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-10-25 16:02:19.536][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-10-25 16:02:19.538][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-10-25 16:02:19.543][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-10-25 16:02:19.544][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-10-25 16:02:19.545][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-10-25 16:02:19.546][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-10-25 16:02:19.547][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-10-25 16:02:19.548][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-10-25 16:02:19.549][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-10-25 16:02:19.550][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-10-25 16:02:19.551][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-10-25 16:02:19.553][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-10-25 16:02:19.554][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-10-25 16:02:19.555][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-10-25 16:02:19.556][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-10-25 16:02:19.557][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-10-25 16:02:19.558][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-10-25 16:02:19.559][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-10-25 16:02:19.560][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-10-25 16:02:19.561][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-10-25 16:02:19.562][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-10-25 16:02:19.563][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-10-25 16:02:19.564][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-10-25 16:02:19.565][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-10-25 16:02:19.566][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-10-25 16:02:19.567][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-10-25 16:02:19.569][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-10-25 16:02:19.570][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-10-25 16:02:19.571][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-10-25 16:02:19.572][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-10-25 16:02:19.573][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-10-25 16:02:19.574][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-10-25 16:02:19.575][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-10-25 16:02:19.576][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-10-25 16:02:19.577][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-10-25 16:02:19.578][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-10-25 16:02:19.579][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-10-25 16:02:19.580][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-10-25 16:02:19.582][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-10-25 16:02:19.583][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-10-25 16:02:19.584][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-10-25 16:02:19.585][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-10-25 16:02:19.586][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-10-25 16:02:19.587][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-10-25 16:02:19.588][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-10-25 16:02:19.589][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-10-25 16:02:19.590][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-10-25 16:02:19.591][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-10-25 16:02:19.592][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-10-25 16:02:19.593][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-10-25 16:02:19.594][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-10-25 16:02:19.595][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-10-25 16:02:19.596][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-10-25 16:02:19.597][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-10-25 16:02:19.598][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-10-25 16:02:19.599][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-10-25 16:02:19.600][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-10-25 16:02:19.601][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-10-25 16:02:19.602][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-10-25 16:02:19.603][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-10-25 16:02:19.604][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-10-25 16:02:19.605][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-10-25 16:02:19.606][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-10-25 16:02:19.608][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-10-25 16:02:19.609][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-10-25 16:02:19.610][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-10-25 16:02:19.611][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-10-25 16:02:19.612][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-10-25 16:02:19.613][initialize] This is biodb version 1.17.2.
biodb.DEBUG[2025-10-25 16:02:19.614][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-10-25 16:02:19.615][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.616][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.622][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[2025-10-25 16:02:19.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-10-25 16:02:19.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-10-25 16:02:19.700][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-10-25 16:02:19.701][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-10-25 16:02:19.703][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.703][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-10-25 16:02:19.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-10-25 16:02:19.706][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.706][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-10-25 16:02:19.707][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.708][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.709][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-10-25 16:02:19.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-10-25 16:02:19.710][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.711][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-10-25 16:02:19.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-10-25 16:02:19.713][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-10-25 16:02:19.714][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.715][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-10-25 16:02:19.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.717][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-10-25 16:02:19.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-10-25 16:02:19.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-10-25 16:02:19.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-10-25 16:02:19.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:02:19.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-10-25 16:02:19.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-10-25 16:02:19.724][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-10-25 16:02:19.725][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-10-25 16:02:19.726][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-10-25 16:02:19.726][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-10-25 16:02:19.727][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-10-25 16:02:19.732][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-10-25 16:02:19.734][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-10-25 16:02:19.737][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-10-25 16:02:19.738][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-10-25 16:02:19.739][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-10-25 16:02:19.739][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-10-25 16:02:19.740][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-10-25 16:02:19.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-10-25 16:02:19.741][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-10-25 16:02:19.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-10-25 16:02:19.743][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-10-25 16:02:19.743][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".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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