Back to Long Tests report for BioC 3.22

This page was generated on 2026-04-04 23:55 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 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 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-04-04 09:55 -0400 (Sat, 04 Apr 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-04-04 16:02:16 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 16:03:20 -0400 (Sat, 04 Apr 2026)
EllapsedTime: 64.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-pc-linux-gnu

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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 [2026-04-04 16:03:16.537][biodb::testContext]
biodb.INFO [2026-04-04 16:03:16.539][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:03:16.540][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-04-04 16:03:16.541][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:03:16.542][biodb::testContext]
biodb.INFO [2026-04-04 16:03:16.547][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:03:16.549][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:03:16.555][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:16.556][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:03:16.557][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.561][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:03:16.577][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.580][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:03:16.581][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.585][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:03:16.585][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:03:16.586][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:03:16.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.590][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:03:16.591][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:03:16.592][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.595][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:03:16.596][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:03:16.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.599][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:03:16.600][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:03:16.601][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:03:16.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.605][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:03:16.606][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.609][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:03:16.610][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:03:16.611][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:03:16.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.614][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:03:16.615][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:03:16.616][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:03:16.617][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:03:16.618][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:03:16.619][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:03:16.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.622][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:03:16.623][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:03:16.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.627][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:03:16.628][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:03:16.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.631][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:03:16.632][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:03:16.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.635][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:03:16.636][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:03:16.637][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:03:16.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.641][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:03:16.641][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:03:16.645][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:03:16.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.648][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:03:16.649][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:03:16.650][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:03:16.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.656][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:03:16.686][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.707][self$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[2026-04-04 16:03:16.708][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.709][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:16.710][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.711][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.711][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.713][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:03:16.714][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:16.715][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.716][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:03:16.717][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:16.718][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.719][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.720][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:03:16.720][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:03:16.720][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:03:16.720][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:03:16.720][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:03:16.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:16.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.723][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:16.724][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.726][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.727][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.728][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:16.729][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:16.730][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.730][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:03:16.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.734][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:03:16.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:16.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.739][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.741][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:03:16.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:16.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.743][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:03:16.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:16.745][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.746][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.747][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:03:16.747][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:03:16.747][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:03:16.747][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:03:16.747][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:03:16.748][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:16.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:16.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.753][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.754][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.755][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:16.756][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:16.757][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.758][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.759][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:03:16.761][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.761][self$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[2026-04-04 16:03:16.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:16.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.765][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.768][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:03:16.769][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:16.770][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.771][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:03:16.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:16.773][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.774][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.774][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.775][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:16.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.777][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.778][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:16.779][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.780][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.782][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:16.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:16.784][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.785][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.786][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:03:16.788][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.789][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:03:16.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:16.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.795][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:03:16.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:16.797][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.798][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:03:16.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:16.800][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:16.802][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.803][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:16.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:16.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:16.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:16.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:16.809][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.810][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:16.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:16.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:16.812][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:16.816][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:16.817][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:16.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:16.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:16.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:16.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:16.885][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:03:16.890][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:03:16.891][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:03:16.892][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:03:16.894][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:03:16.895][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:03:16.896][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:03:16.898][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:03:16.899][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:03:16.900][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:03:16.902][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:03:16.925][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:03:16.926][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:03:16.928][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:03:16.929][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:03:16.931][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:03:16.932][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:03:16.934][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:03:16.935][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:03:16.937][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:03:16.938][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:03:16.940][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:03:16.941][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:03:16.942][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:03:16.944][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:03:16.945][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:03:16.947][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:03:16.948][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:03:16.950][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:03:16.951][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:03:16.953][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:03:16.954][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:03:16.956][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:03:16.957][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:03:16.958][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:03:16.960][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:03:16.961][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:03:16.963][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:03:16.964][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:03:16.965][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:03:16.967][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:03:16.968][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:03:16.970][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:03:16.971][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:03:16.973][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:03:16.974][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:03:16.975][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:03:16.977][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:03:16.978][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:03:16.980][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:03:16.981][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:03:16.983][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:03:16.984][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:03:16.985][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:03:16.987][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:03:16.988][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:03:16.990][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:03:16.991][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:03:16.992][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:03:16.994][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:03:16.995][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:03:16.997][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:03:16.998][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:03:16.999][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:03:17.001][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:03:17.002][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:03:17.004][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:03:17.005][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:03:17.006][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:03:17.008][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:03:17.009][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:03:17.011][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:03:17.012][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:03:17.013][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:03:17.015][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:03:17.016][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:03:17.017][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:03:17.019][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:03:17.020][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:03:17.022][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:03:17.023][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:03:17.025][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:03:17.026][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:03:17.032][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:03:17.034][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:03:17.037][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:17.038][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.040][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:17.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:17.150][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-04-04 16:03:17.159][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-04-04 16:03:17.161][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:17.162][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-04-04 16:03:17.163][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:17.164][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:17.165][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:17.166][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-04-04 16:03:17.167][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:17.168][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:17.169][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-04-04 16:03:17.169][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:17.170][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:17.171][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-04-04 16:03:17.172][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-04-04 16:03:17.173][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-04-04 16:03:17.174][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:17.175][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:17.176][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:03:17.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:17.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:17.179][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:17.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:17.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:17.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:17.183][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:03:17.183][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:03:17.183][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-04-04 16:03:17.183][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-04-04 16:03:17.184][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:17.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:17.185][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:17.186][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:17.192][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-04-04 16:03:17.213][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-04-04 16:03:17.227][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-04-04 16:03:17.235][biodb::testThat]
biodb.INFO [2026-04-04 16:03:17.236][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:03:17.237][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:17.238][biodb::testThat]
biodb.TRACE[2026-04-04 16:03:17.241][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-04-04 16:03:17.243][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:03:17.246][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-04-04 16:03:17.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:03:17.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:03:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.371][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.375][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.383][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:03:17.440][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-04-04 16:03:17.442][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.446][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:03:17.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:03:17.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.453][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:03:17.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:03:17.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.473][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.508][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.512][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.516][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.536][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.537][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.538][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.539][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.562][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.564][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.564][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.587][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.588][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.589][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.590][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.612][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.613][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.614][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.615][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.637][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.638][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.639][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.640][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.651][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.652][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.654][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.658][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.660][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.661][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.664][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.669][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.670][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.671][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.675][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.676][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.677][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.678][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.681][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.682][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.683][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.684][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.700][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-04-04 16:03:17.732][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:03:17.734][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-04-04 16:03:17.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:03:17.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:17.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:17.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:17.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:17.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:17.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-04-04 16:03:17.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.777][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:17.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:17.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:17.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:17.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:17.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:17.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:17.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.883][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.887][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:03:17.920][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-04-04 16:03:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:03:17.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:03:17.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:03:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:03:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:03:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.962][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:17.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.993][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:17.997][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:17.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:18.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-04-04 16:03:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.034][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.035][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.036][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.036][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.052][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.059][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.060][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.061][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.062][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.063][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.085][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.087][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.088][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.110][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.111][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.112][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.113][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.135][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.137][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.138][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.162][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.163][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.189][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.190][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.191][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.192][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.204][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:03:18.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:03:18.205][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.206][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.210][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.211][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:03:18.212][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.213][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.217][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:03:18.218][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:03:18.219][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.220][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.223][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:03:18.224][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:03:18.225][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.226][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.230][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.231][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:03:18.232][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.233][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.237][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.238][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-04-04 16:03:18.239][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.239][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:03:18.243][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:03:18.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:03:18.245][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:03:18.246][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:03:18.252][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.253][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:03:18.254][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.255][biodb::testThat]
biodb.DEBUG[2026-04-04 16:03:18.257][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-04-04 16:03:18.260][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-04-04 16:03:18.263][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-04-04 16:03:18.290][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-04-04 16:03:18.292][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-04-04 16:03:18.293][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-04-04 16:03:18.420][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.421][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:03:18.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.423][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.428][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.429][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:03:18.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.431][biodb::testThat]
biodb.WARN [2026-04-04 16:03:18.446][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-04-04 16:03:18.467][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-04-04 16:03:18.474][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.475][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:03:18.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.477][biodb::testThat]
biodb.DEBUG[2026-04-04 16:03:18.492][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-04-04 16:03:18.536][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:03:18.537][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-04-04 16:03:18.538][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-04-04 16:03:18.540][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-04-04 16:03:18.551][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-04-04 16:03:18.606][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.607][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:03:18.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.609][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.616][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.617][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:03:18.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.619][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.625][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.626][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:03:18.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.628][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.634][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.635][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:03:18.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:03:18.636][biodb::testThat]
biodb.INFO [2026-04-04 16:03:18.642][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:03:18.643][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-04-04 16:03:18.644][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:03:18.645][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:18.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:18.646][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.648][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-04-04 16:03:18.658][biodb::testContext]
biodb.INFO [2026-04-04 16:03:18.659][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:03:18.660][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-04-04 16:03:18.661][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:03:18.661][biodb::testContext]
biodb.INFO [2026-04-04 16:03:18.663][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:03:18.665][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:03:18.668][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:18.669][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:03:18.670][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.674][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:03:18.675][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.678][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:03:18.679][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.683][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:03:18.684][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:03:18.685][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:03:18.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.688][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:03:18.689][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:03:18.690][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.693][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:03:18.694][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:03:18.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.698][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:03:18.699][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:03:18.700][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:03:18.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.703][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:03:18.704][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.708][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:03:18.709][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:03:18.710][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:03:18.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.713][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:03:18.714][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:03:18.715][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:03:18.716][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:03:18.717][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:03:18.718][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:03:18.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.721][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:03:18.722][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:03:18.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.725][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[2026-04-04 16:03:18.726][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:03:18.727][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:03:18.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.730][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:03:18.731][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:03:18.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.735][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:03:18.735][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:03:18.736][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:03:18.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.740][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:03:18.745][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:03:18.749][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:03:18.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.752][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:03:18.753][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:03:18.754][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:03:18.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.758][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:03:18.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.760][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-04-04 16:03:18.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.762][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:18.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.764][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.765][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.767][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:03:18.768][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:18.769][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.770][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:03:18.771][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:18.772][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.774][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:03:18.774][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:03:18.774][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:03:18.774][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:03:18.774][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:03:18.775][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:18.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.777][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:18.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.780][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.781][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.782][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:18.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:18.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.784][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:03:18.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.788][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:03:18.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.790][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:18.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.795][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:03:18.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:18.796][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.797][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:03:18.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:18.799][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:03:18.801][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:03:18.801][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:03:18.801][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:03:18.801][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:03:18.802][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:18.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:18.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.808][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.809][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:18.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:18.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.812][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.813][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:03:18.815][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.816][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-04-04 16:03:18.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:18.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.820][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.822][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:03:18.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:18.824][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.825][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:03:18.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:18.827][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.828][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.829][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:18.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.832][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:18.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.835][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.836][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.837][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:18.837][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:18.838][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.839][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.840][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:03:18.842][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.843][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:03:18.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:18.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.849][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:03:18.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:18.851][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.852][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:03:18.853][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:18.854][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.855][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:18.856][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.857][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:03:18.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:18.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:18.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:18.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:18.863][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.864][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:18.865][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:18.866][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:18.867][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:18.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:18.869][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.886][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[2026-04-04 16:03:18.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.923][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[2026-04-04 16:03:18.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.932][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[2026-04-04 16:03:18.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:18.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:18.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:18.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:18.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:18.941][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:03:18.942][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:03:18.944][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:03:18.945][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:03:18.946][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:03:18.948][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:03:18.949][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:03:18.950][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:03:18.951][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:03:18.953][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:03:18.954][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:03:18.955][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:03:18.957][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:03:18.958][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:03:18.959][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:03:18.961][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:03:18.962][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:03:18.963][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:03:18.964][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:03:18.966][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:03:18.967][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:03:18.968][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:03:18.970][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:03:18.971][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:03:18.972][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:03:18.974][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:03:18.975][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:03:18.976][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:03:18.977][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:03:18.979][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:03:18.980][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:03:18.981][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:03:18.983][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:03:18.984][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:03:18.985][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:03:18.987][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:03:18.988][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:03:18.989][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:03:18.990][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:03:18.992][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:03:18.993][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:03:18.994][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:03:18.996][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:03:18.997][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:03:18.998][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:03:19.000][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:03:19.001][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:03:19.002][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:03:19.004][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:03:19.005][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:03:19.006][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:03:19.007][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:03:19.009][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:03:19.010][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:03:19.011][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:03:19.013][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:03:19.014][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:03:19.015][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:03:19.016][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:03:19.018][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:03:19.019][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:03:19.020][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:03:19.022][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:03:19.023][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:03:19.024][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:03:19.025][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:03:19.027][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:03:19.028][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:03:19.029][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:03:19.031][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:03:19.032][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:03:19.033][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:03:19.035][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:03:19.036][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:03:19.037][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:03:19.038][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:03:19.040][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:03:19.045][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:03:19.046][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:03:19.048][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:03:19.049][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:03:19.050][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:03:19.051][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:03:19.053][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:03:19.054][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:03:19.055][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:03:19.056][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.058][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:03:19.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:03:19.153][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-04-04 16:03:19.154][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-04-04 16:03:19.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:19.157][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-04-04 16:03:19.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:19.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:03:19.160][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:19.161][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-04-04 16:03:19.162][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:19.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:03:19.164][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-04-04 16:03:19.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:03:19.166][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:19.167][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-04-04 16:03:19.168][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-04-04 16:03:19.169][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:03:19.170][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:19.171][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:03:19.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:19.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:19.174][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:03:19.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:03:19.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:03:19.177][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:03:19.177][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:03:19.177][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-04-04 16:03:19.177][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-04-04 16:03:19.177][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-04-04 16:03:19.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:03:19.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:03:19.180][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:03:19.181][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:03:19.182][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-04-04 16:03:19.185][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-04-04 16:03:19.192][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-04-04 16:03:19.193][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:03:19.194][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-04-04 16:03:19.195][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:03:19.196][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:03:19.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:03:19.197][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:03:19.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:03:19.199][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:03:19.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/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)