Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-14 23:55 -0400 (Sat, 14 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4686
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: 2026-03-14 09:55 -0400 (Sat, 14 Mar 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 merida1

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-03-14 16:01:15 -0400 (Sat, 14 Mar 2026)
EndedAt: 2026-03-14 16:02:42 -0400 (Sat, 14 Mar 2026)
EllapsedTime: 87.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-03-14 16:02:37.749][biodb::testContext]
biodb.INFO [2026-03-14 16:02:37.753][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-14 16:02:37.754][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-14 16:02:37.755][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-14 16:02:37.757][biodb::testContext]
biodb.INFO [2026-03-14 16:02:37.763][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-14 16:02:37.765][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-14 16:02:37.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:37.774][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-14 16:02:37.775][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.780][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-14 16:02:37.805][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.809][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-14 16:02:37.811][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.815][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-14 16:02:37.817][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-14 16:02:37.818][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-14 16:02:37.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.823][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-14 16:02:37.824][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-14 16:02:37.825][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.830][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-14 16:02:37.831][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-14 16:02:37.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.836][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-14 16:02:37.837][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-14 16:02:37.838][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-14 16:02:37.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.843][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-14 16:02:37.844][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.849][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-14 16:02:37.850][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-14 16:02:37.851][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-14 16:02:37.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.856][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-14 16:02:37.857][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-14 16:02:37.859][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-14 16:02:37.860][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-14 16:02:37.861][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-14 16:02:37.862][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-14 16:02:37.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.868][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-14 16:02:37.869][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-14 16:02:37.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.874][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-14 16:02:37.875][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-14 16:02:37.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.880][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-14 16:02:37.881][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-14 16:02:37.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.886][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-14 16:02:37.887][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-14 16:02:37.889][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-14 16:02:37.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.893][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-14 16:02:37.894][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-14 16:02:37.905][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-14 16:02:37.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:37.910][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-14 16:02:37.911][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-14 16:02:37.912][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-14 16:02:37.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:37.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:37.915][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[2026-03-14 16:02:37.919][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-14 16:02:37.963][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:37.991][self$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[2026-03-14 16:02:37.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:37.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:37.995][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:37.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:37.997][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:37.998][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.000][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-14 16:02:38.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:38.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.003][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-14 16:02:38.005][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:38.006][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.007][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-14 16:02:38.008][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-14 16:02:38.008][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-14 16:02:38.008][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-14 16:02:38.008][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-14 16:02:38.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:38.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:38.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.018][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:38.020][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:38.021][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.023][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.024][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-14 16:02:38.026][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.028][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-14 16:02:38.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:38.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.035][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.036][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-14 16:02:38.037][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:38.039][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.040][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-14 16:02:38.041][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:38.042][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.045][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-14 16:02:38.045][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-14 16:02:38.045][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-14 16:02:38.045][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-14 16:02:38.045][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-14 16:02:38.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:38.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.050][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:38.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.053][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.054][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.056][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:38.057][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:38.058][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.059][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.061][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-14 16:02:38.063][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.064][self$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[2026-03-14 16:02:38.065][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.067][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:38.068][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.069][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.071][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.072][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.073][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-14 16:02:38.075][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:38.076][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.077][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-14 16:02:38.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:38.080][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.082][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.083][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:38.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:38.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.093][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:38.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:38.097][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.098][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.099][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-14 16:02:38.102][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.103][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-14 16:02:38.104][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:38.107][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.108][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.109][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.112][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-14 16:02:38.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:38.114][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.115][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-14 16:02:38.117][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:38.118][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.120][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:38.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:38.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.130][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:38.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:38.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.135][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.138][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:38.140][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.146][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[2026-03-14 16:02:38.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.152][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[2026-03-14 16:02:38.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.200][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".
biodb.DEBUG[2026-03-14 16:02:38.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.229][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-14 16:02:38.233][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-14 16:02:38.235][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-14 16:02:38.241][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-14 16:02:38.243][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-14 16:02:38.245][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-14 16:02:38.246][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-14 16:02:38.248][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-14 16:02:38.249][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-14 16:02:38.251][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-14 16:02:38.253][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-14 16:02:38.254][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-14 16:02:38.256][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-14 16:02:38.258][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-14 16:02:38.259][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-14 16:02:38.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-14 16:02:38.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-14 16:02:38.264][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-14 16:02:38.266][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-14 16:02:38.268][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-14 16:02:38.270][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-14 16:02:38.271][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-14 16:02:38.273][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-14 16:02:38.275][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-14 16:02:38.276][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-14 16:02:38.278][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-14 16:02:38.280][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-14 16:02:38.281][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-14 16:02:38.283][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-14 16:02:38.285][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-14 16:02:38.287][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-14 16:02:38.288][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-14 16:02:38.290][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-14 16:02:38.292][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-14 16:02:38.293][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-14 16:02:38.295][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-14 16:02:38.297][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-14 16:02:38.298][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-14 16:02:38.300][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-14 16:02:38.302][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-14 16:02:38.303][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-14 16:02:38.305][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-14 16:02:38.307][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-14 16:02:38.308][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-14 16:02:38.310][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-14 16:02:38.312][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-14 16:02:38.313][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-14 16:02:38.315][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-14 16:02:38.317][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-14 16:02:38.319][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-14 16:02:38.320][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-14 16:02:38.322][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-14 16:02:38.324][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-14 16:02:38.325][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-14 16:02:38.327][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-14 16:02:38.329][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-14 16:02:38.330][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-14 16:02:38.332][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-14 16:02:38.334][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-14 16:02:38.335][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-14 16:02:38.337][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-14 16:02:38.339][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-14 16:02:38.341][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-14 16:02:38.342][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-14 16:02:38.344][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-14 16:02:38.346][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-14 16:02:38.348][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-14 16:02:38.349][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-14 16:02:38.351][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-14 16:02:38.353][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-14 16:02:38.355][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-14 16:02:38.356][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-14 16:02:38.358][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-14 16:02:38.360][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-14 16:02:38.362][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-14 16:02:38.363][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-14 16:02:38.365][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-14 16:02:38.367][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-14 16:02:38.369][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-14 16:02:38.371][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-14 16:02:38.372][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-14 16:02:38.374][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-14 16:02:38.376][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-14 16:02:38.384][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-14 16:02:38.386][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-14 16:02:38.389][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:38.390][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.392][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:38.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:38.527][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-14 16:02:38.540][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-14 16:02:38.542][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.544][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-14 16:02:38.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:38.547][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.549][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-14 16:02:38.550][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.552][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-14 16:02:38.553][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:38.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.556][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-14 16:02:38.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-14 16:02:38.558][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-14 16:02:38.560][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:38.561][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.562][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-14 16:02:38.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:38.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:38.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:38.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:38.570][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-14 16:02:38.570][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-14 16:02:38.570][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-14 16:02:38.570][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-14 16:02:38.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:38.573][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:38.574][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:38.575][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:38.583][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-14 16:02:38.605][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-14 16:02:38.621][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-14 16:02:38.631][biodb::testThat]
biodb.INFO [2026-03-14 16:02:38.633][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-14 16:02:38.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:38.635][biodb::testThat]
biodb.TRACE[2026-03-14 16:02:38.639][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-03-14 16:02:38.642][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-14 16:02:38.645][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-14 16:02:38.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-14 16:02:38.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:38.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:38.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:38.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:38.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:38.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-14 16:02:38.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:38.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:38.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:38.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:38.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:38.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:38.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:38.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:38.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:38.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:38.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:38.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:38.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:38.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.812][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.817][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.827][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-14 16:02:38.905][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-03-14 16:02:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-14 16:02:38.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-14 16:02:38.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.914][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-14 16:02:38.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-14 16:02:38.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-14 16:02:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-14 16:02:38.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-14 16:02:38.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-14 16:02:38.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.951][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:38.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:38.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:38.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:38.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:38.998][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.003][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.008][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.037][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.039][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.041][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.073][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.075][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.077][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.108][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.110][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.111][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.112][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.145][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.146][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.147][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.181][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.182][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.183][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.204][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.207][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.208][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.214][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.216][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.217][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.218][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.225][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.227][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.228][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.234][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.235][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.237][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.238][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.244][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.246][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.247][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.248][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.271][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-03-14 16:02:39.319][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-14 16:02:39.320][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-14 16:02:39.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-14 16:02:39.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:39.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:39.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:39.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:39.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:39.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-14 16:02:39.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.386][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.511][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.516][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.526][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-14 16:02:39.561][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-03-14 16:02:39.589][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-14 16:02:39.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-14 16:02:39.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.594][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-14 16:02:39.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-14 16:02:39.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-14 16:02:39.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-14 16:02:39.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-14 16:02:39.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-14 16:02:39.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.621][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.673][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-14 16:02:39.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.726][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.729][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.730][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.758][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.764][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.766][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.767][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.768][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.769][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.802][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.804][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.805][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:39.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:39.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.838][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.839][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.840][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.841][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.843][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.874][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.875][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.876][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.878][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:39.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.916][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.918][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.919][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:39.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.954][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.955][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:39.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.973][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-14 16:02:39.974][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-14 16:02:39.976][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.977][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.985][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.986][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-14 16:02:39.988][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:39.989][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:39.996][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-14 16:02:39.997][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-14 16:02:39.999][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:40.000][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:40.006][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-14 16:02:40.008][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-14 16:02:40.009][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:40.010][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:40.017][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-14 16:02:40.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-14 16:02:40.019][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:40.020][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:40.027][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:40.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-14 16:02:40.029][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:40.030][ef$get] fields variable is a list.
biodb.TRACE[2026-03-14 16:02:40.037][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-14 16:02:40.038][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-14 16:02:40.039][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-14 16:02:40.041][ef$get] fields variable is a list.
biodb.INFO [2026-03-14 16:02:40.051][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.052][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-14 16:02:40.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.055][biodb::testThat]
biodb.DEBUG[2026-03-14 16:02:40.058][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-03-14 16:02:40.063][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-03-14 16:02:40.066][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-14 16:02:40.105][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-14 16:02:40.107][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-14 16:02:40.108][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-14 16:02:40.282][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.283][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-14 16:02:40.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.286][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.294][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.295][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-14 16:02:40.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.297][biodb::testThat]
biodb.WARN [2026-03-14 16:02:40.326][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-14 16:02:40.350][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-14 16:02:40.360][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.361][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-14 16:02:40.362][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.364][biodb::testThat]
biodb.DEBUG[2026-03-14 16:02:40.386][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-03-14 16:02:40.449][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-14 16:02:40.451][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-14 16:02:40.453][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-14 16:02:40.454][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-14 16:02:40.471][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-14 16:02:40.547][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.549][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-14 16:02:40.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.551][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.561][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.562][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-14 16:02:40.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.564][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.574][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.575][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-14 16:02:40.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.578][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.586][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.587][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-14 16:02:40.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-14 16:02:40.590][biodb::testThat]
biodb.INFO [2026-03-14 16:02:40.598][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-14 16:02:40.599][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-14 16:02:40.600][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-14 16:02:40.601][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:40.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:40.603][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.606][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-14 16:02:40.619][biodb::testContext]
biodb.INFO [2026-03-14 16:02:40.621][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-14 16:02:40.622][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-03-14 16:02:40.623][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-14 16:02:40.624][biodb::testContext]
biodb.INFO [2026-03-14 16:02:40.627][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-14 16:02:40.629][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-14 16:02:40.633][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:40.634][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-14 16:02:40.635][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.640][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-14 16:02:40.641][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.646][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-14 16:02:40.647][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.651][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-14 16:02:40.653][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-14 16:02:40.654][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-14 16:02:40.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.658][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-14 16:02:40.660][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-14 16:02:40.661][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.665][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-14 16:02:40.667][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-14 16:02:40.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.671][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-14 16:02:40.672][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-14 16:02:40.674][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-14 16:02:40.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.677][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[2026-03-14 16:02:40.678][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-14 16:02:40.679][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.684][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-14 16:02:40.685][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-14 16:02:40.686][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-14 16:02:40.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.696][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-14 16:02:40.697][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-14 16:02:40.698][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-14 16:02:40.700][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-14 16:02:40.701][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-14 16:02:40.702][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-14 16:02:40.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.707][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-14 16:02:40.708][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-14 16:02:40.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.712][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-14 16:02:40.714][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-14 16:02:40.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.718][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-14 16:02:40.719][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-14 16:02:40.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.724][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-14 16:02:40.725][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-14 16:02:40.727][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-14 16:02:40.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.731][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-14 16:02:40.733][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-14 16:02:40.743][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-14 16:02:40.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.748][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-14 16:02:40.749][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-14 16:02:40.750][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-14 16:02:40.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.755][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-14 16:02:40.757][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.759][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-14 16:02:40.760][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.761][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:40.762][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.763][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.765][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.767][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-14 16:02:40.768][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:40.770][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.771][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-14 16:02:40.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:40.773][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.775][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.776][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-14 16:02:40.776][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-14 16:02:40.776][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-14 16:02:40.776][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-14 16:02:40.776][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-14 16:02:40.777][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:40.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.781][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:40.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.784][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.785][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:40.788][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:40.789][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.790][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.791][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-14 16:02:40.794][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.795][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-14 16:02:40.796][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.797][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:40.799][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.800][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.801][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.802][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.803][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-14 16:02:40.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:40.806][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.807][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-14 16:02:40.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:40.810][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.811][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.812][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-14 16:02:40.812][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-14 16:02:40.812][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-14 16:02:40.812][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-14 16:02:40.812][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-14 16:02:40.813][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:40.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:40.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.820][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.821][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.823][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:40.824][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:40.825][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.826][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.828][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-14 16:02:40.830][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.831][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-14 16:02:40.832][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.833][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:40.835][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.836][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.837][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.840][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-14 16:02:40.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:40.842][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.843][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-14 16:02:40.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:40.846][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.848][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:40.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:40.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.858][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:40.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:40.861][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.862][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.864][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-14 16:02:40.866][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.867][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-14 16:02:40.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:40.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.874][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.876][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-14 16:02:40.877][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:40.878][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.879][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-14 16:02:40.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:40.882][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.883][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:40.884][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.886][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-14 16:02:40.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:40.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:40.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:40.893][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:40.894][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:40.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:40.902][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:40.904][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:40.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:40.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.919][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[2026-03-14 16:02:40.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.936][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[2026-03-14 16:02:40.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:40.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:40.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:40.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:40.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:40.999][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-14 16:02:41.001][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-14 16:02:41.003][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-14 16:02:41.005][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-14 16:02:41.007][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-14 16:02:41.009][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-14 16:02:41.011][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-14 16:02:41.013][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-14 16:02:41.014][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-14 16:02:41.016][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-14 16:02:41.018][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-14 16:02:41.019][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-14 16:02:41.021][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-14 16:02:41.023][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-14 16:02:41.024][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-14 16:02:41.026][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-14 16:02:41.028][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-14 16:02:41.030][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-14 16:02:41.031][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-14 16:02:41.033][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-14 16:02:41.035][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-14 16:02:41.036][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-14 16:02:41.038][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-14 16:02:41.040][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-14 16:02:41.042][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-14 16:02:41.043][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-14 16:02:41.045][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-14 16:02:41.047][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-14 16:02:41.049][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-14 16:02:41.050][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-14 16:02:41.052][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-14 16:02:41.054][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-14 16:02:41.055][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-14 16:02:41.057][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-14 16:02:41.059][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-14 16:02:41.060][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-14 16:02:41.062][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-14 16:02:41.064][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-14 16:02:41.065][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-14 16:02:41.067][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-14 16:02:41.069][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-14 16:02:41.071][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-14 16:02:41.072][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-14 16:02:41.074][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-14 16:02:41.076][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-14 16:02:41.077][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-14 16:02:41.079][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-14 16:02:41.081][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-14 16:02:41.082][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-14 16:02:41.084][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-14 16:02:41.086][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-14 16:02:41.087][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-14 16:02:41.094][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-14 16:02:41.096][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-14 16:02:41.097][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-14 16:02:41.099][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-14 16:02:41.101][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-14 16:02:41.102][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-14 16:02:41.104][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-14 16:02:41.106][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-14 16:02:41.107][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-14 16:02:41.109][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-14 16:02:41.111][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-14 16:02:41.112][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-14 16:02:41.114][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-14 16:02:41.116][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-14 16:02:41.117][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-14 16:02:41.119][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-14 16:02:41.121][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-14 16:02:41.122][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-14 16:02:41.124][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-14 16:02:41.126][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-14 16:02:41.128][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-14 16:02:41.129][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-14 16:02:41.131][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-14 16:02:41.133][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-14 16:02:41.134][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-14 16:02:41.136][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-14 16:02:41.138][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-14 16:02:41.139][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-14 16:02:41.141][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-14 16:02:41.143][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-14 16:02:41.144][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-14 16:02:41.146][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-14 16:02:41.148][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-14 16:02:41.149][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-14 16:02:41.150][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.153][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.200][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".
biodb.DEBUG[2026-03-14 16:02:41.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-14 16:02:41.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-14 16:02:41.283][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-14 16:02:41.285][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-14 16:02:41.288][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:41.289][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-14 16:02:41.290][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:41.292][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-14 16:02:41.293][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:41.294][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-14 16:02:41.295][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:41.296][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-14 16:02:41.298][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-14 16:02:41.299][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-14 16:02:41.300][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:41.301][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-14 16:02:41.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-14 16:02:41.304][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-14 16:02:41.305][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-14 16:02:41.306][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:41.308][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-14 16:02:41.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:41.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:41.311][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-14 16:02:41.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-14 16:02:41.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-14 16:02:41.315][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-14 16:02:41.316][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-14 16:02:41.316][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-14 16:02:41.316][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-14 16:02:41.316][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-14 16:02:41.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-14 16:02:41.318][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-14 16:02:41.319][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-14 16:02:41.321][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-14 16:02:41.322][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-14 16:02:41.326][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-14 16:02:41.330][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-14 16:02:41.332][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-14 16:02:41.333][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-14 16:02:41.334][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-14 16:02:41.335][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-14 16:02:41.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-14 16:02:41.337][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-14 16:02:41.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-14 16:02:41.340][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-14 16:02:41.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbNci.Rcheck/00install.out

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