Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-06 23:55 -0500 (Sat, 06 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4668
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-06 09:55 -0500 (Sat, 06 Dec 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2025-12-06 16:02:23 -0500 (Sat, 06 Dec 2025)
EndedAt: 2025-12-06 16:03:28 -0500 (Sat, 06 Dec 2025)
EllapsedTime: 65.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-12-06 16:03:24.595][biodb::testContext]
biodb.INFO [2025-12-06 16:03:24.597][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:24.598][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-06 16:03:24.599][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:24.600][biodb::testContext]
biodb.INFO [2025-12-06 16:03:24.606][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:24.608][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:24.614][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:24.615][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:03:24.616][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.620][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:03:24.636][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.639][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[2025-12-06 16:03:24.640][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:03:24.641][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.653][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:03:24.654][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:03:24.655][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:03:24.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.657][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[2025-12-06 16:03:24.658][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:03:24.659][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:03:24.660][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.663][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:03:24.664][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:03:24.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.668][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:03:24.669][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:03:24.670][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:03:24.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.673][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:03:24.674][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.677][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[2025-12-06 16:03:24.677][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:03:24.678][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:03:24.679][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:03:24.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.683][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:24.684][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:03:24.685][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:03:24.685][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:03:24.686][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:03:24.687][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:03:24.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.691][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:03:24.692][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:03:24.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.695][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:03:24.696][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:03:24.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.699][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:03:24.700][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:03:24.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.703][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:03:24.704][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:03:24.705][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:03:24.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.709][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:24.710][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:03:24.714][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:03:24.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.718][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:03:24.719][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:03:24.720][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:03:24.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.725][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:03:24.756][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.770][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:03:24.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:24.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.775][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.777][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:24.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:24.779][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.779][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:03:24.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:24.781][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.782][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.783][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:24.783][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:24.783][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:24.783][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:24.783][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:24.784][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:24.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.787][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:24.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.789][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.790][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:24.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:24.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.794][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.795][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:03:24.796][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.797][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:24.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.799][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:24.800][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.801][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.802][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.803][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.808][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:24.809][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:24.810][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.811][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:03:24.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:24.813][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:24.814][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:24.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:24.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.818][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:24.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.822][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:24.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:24.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.825][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.826][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:03:24.828][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.829][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:03:24.830][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.831][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:24.831][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.832][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.833][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.835][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:24.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:24.837][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.838][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:03:24.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:24.840][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.841][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.842][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.842][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:24.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.845][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:24.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.848][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.848][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.849][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:24.850][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:24.851][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.852][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.853][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:03:24.855][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.856][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:24.856][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.857][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:24.858][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.860][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.862][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:24.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:24.864][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.865][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:03:24.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:24.866][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:24.868][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.869][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:24.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.872][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:24.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:24.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:24.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:24.875][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:24.877][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:24.878][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:24.879][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:24.882][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:24.883][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.892][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[2025-12-06 16:03:24.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.908][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[2025-12-06 16:03:24.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.913][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[2025-12-06 16:03:24.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:24.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:24.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:24.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:24.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:24.950][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:03:24.955][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:03:24.956][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:03:24.967][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:03:24.969][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:03:24.989][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:03:24.991][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:24.992][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:24.994][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:03:24.995][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:03:24.997][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:03:24.998][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:03:25.000][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:25.001][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:25.003][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:03:25.004][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:03:25.006][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:03:25.007][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:03:25.009][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:03:25.011][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:03:25.012][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:03:25.013][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:03:25.015][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:03:25.016][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:03:25.018][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:03:25.019][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:03:25.021][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:03:25.022][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:03:25.023][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:03:25.025][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:03:25.026][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:03:25.028][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:03:25.029][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:03:25.030][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:03:25.032][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:03:25.033][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:03:25.035][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:03:25.036][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:03:25.037][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:03:25.039][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:03:25.040][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:03:25.042][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:03:25.043][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:03:25.044][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:03:25.046][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:03:25.047][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:03:25.049][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:03:25.050][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:03:25.051][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:03:25.053][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:03:25.054][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:03:25.056][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:03:25.057][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:03:25.058][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:03:25.060][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:03:25.061][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:03:25.063][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:03:25.064][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:03:25.065][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:03:25.067][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:03:25.068][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:03:25.069][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:03:25.071][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:03:25.072][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:03:25.074][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:03:25.075][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:03:25.076][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:03:25.078][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:03:25.079][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:03:25.080][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:03:25.082][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:03:25.083][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:03:25.085][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:03:25.086][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:03:25.087][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:03:25.089][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:03:25.090][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:03:25.092][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:03:25.093][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:03:25.094][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:03:25.096][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:03:25.097][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:03:25.099][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:03:25.105][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:03:25.107][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:25.110][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:25.111][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.113][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:25.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:25.217][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:25.226][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-06 16:03:25.228][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:25.229][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-06 16:03:25.230][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:25.231][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:25.232][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:25.233][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-06 16:03:25.233][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:25.234][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:25.235][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-06 16:03:25.236][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:25.237][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:25.238][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-06 16:03:25.239][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-06 16:03:25.240][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-06 16:03:25.241][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:25.242][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:25.243][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:03:25.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:25.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:25.245][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:25.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:25.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:25.248][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:25.249][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-06 16:03:25.249][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-06 16:03:25.249][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-06 16:03:25.249][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-06 16:03:25.250][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:25.251][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:25.251][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:25.252][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:25.258][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-06 16:03:25.279][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-06 16:03:25.294][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-06 16:03:25.302][biodb::testThat]
biodb.INFO [2025-12-06 16:03:25.303][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:03:25.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:25.304][biodb::testThat]
biodb.TRACE[2025-12-06 16:03:25.307][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-12-06 16:03:25.309][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:03:25.312][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-06 16:03:25.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:03:25.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:03:25.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.432][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.436][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:03:25.506][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-12-06 16:03:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:25.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:25.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.519][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:25.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.539][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.613][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.616][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.620][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.644][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.659][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.666][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.669][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.670][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.691][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.694][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.717][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.720][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.747][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.748][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.749][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.761][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.764][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.768][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.769][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.770][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.774][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.775][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.777][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.784][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.788][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.789][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.790][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.806][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-12-06 16:03:25.843][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:03:25.845][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-06 16:03:25.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:03:25.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:25.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:25.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:25.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:25.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:25.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:03:25.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.888][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:25.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:25.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.892][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:25.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.900][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:25.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:25.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:25.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:25.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:25.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:25.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:25.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.959][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.970][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:25.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:25.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:25.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:25.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:25.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:03:25.996][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-12-06 16:03:26.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:26.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:26.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.019][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:03:26.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:03:26.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:03:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:03:26.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.038][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.069][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.077][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-06 16:03:26.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.111][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.112][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.113][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.125][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.129][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.133][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.137][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.138][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.140][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.140][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.162][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.165][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.176][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.188][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.189][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.190][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.217][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.220][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.243][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.245][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.268][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.269][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.271][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.282][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:03:26.283][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:03:26.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.285][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.289][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.290][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-06 16:03:26.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.292][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.295][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:03:26.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:03:26.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.298][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.302][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:03:26.303][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:03:26.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.305][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.309][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.310][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:03:26.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.312][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.319][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.320][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:03:26.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.322][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:03:26.326][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:03:26.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:03:26.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:03:26.328][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:03:26.335][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.336][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:03:26.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.337][biodb::testThat]
biodb.DEBUG[2025-12-06 16:03:26.339][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-12-06 16:03:26.341][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-12-06 16:03:26.344][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:26.371][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-06 16:03:26.373][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-06 16:03:26.374][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-06 16:03:26.501][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.503][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:03:26.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.504][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.510][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.511][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:03:26.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.513][biodb::testThat]
biodb.WARN [2025-12-06 16:03:26.535][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-06 16:03:26.553][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-06 16:03:26.561][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.562][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:03:26.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.564][biodb::testThat]
biodb.DEBUG[2025-12-06 16:03:26.580][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-12-06 16:03:26.627][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-06 16:03:26.629][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-06 16:03:26.630][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-06 16:03:26.631][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-06 16:03:26.643][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-06 16:03:26.694][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.696][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:03:26.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.697][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.704][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.705][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:03:26.706][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.707][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.718][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.719][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:03:26.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.721][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.726][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.727][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:03:26.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:03:26.729][biodb::testThat]
biodb.INFO [2025-12-06 16:03:26.734][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:03:26.735][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-06 16:03:26.736][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:03:26.737][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:26.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:26.739][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.740][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-06 16:03:26.750][biodb::testContext]
biodb.INFO [2025-12-06 16:03:26.751][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:26.752][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-12-06 16:03:26.753][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:03:26.754][biodb::testContext]
biodb.INFO [2025-12-06 16:03:26.755][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:26.757][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:26.760][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:26.761][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:03:26.762][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.766][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:03:26.767][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.770][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:03:26.771][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.775][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:03:26.775][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:03:26.776][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:03:26.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.780][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:03:26.781][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:03:26.782][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.785][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:03:26.786][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:03:26.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.790][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:03:26.791][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:03:26.791][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:03:26.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.795][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:03:26.796][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.799][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:03:26.800][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:03:26.801][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:03:26.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.805][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:26.806][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:03:26.807][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:03:26.808][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:03:26.809][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:03:26.810][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:03:26.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.813][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:03:26.814][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:03:26.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.817][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:03:26.818][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:03:26.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.826][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:03:26.827][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:03:26.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.830][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:03:26.831][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:03:26.832][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:03:26.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.836][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:03:26.837][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:03:26.841][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:03:26.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.844][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:03:26.845][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:03:26.846][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:03:26.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.850][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:03:26.851][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.852][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:03:26.853][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:26.855][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.857][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.859][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:26.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:26.861][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.862][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:03:26.863][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:26.864][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.865][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.866][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:26.866][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:26.866][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:26.866][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:26.866][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:26.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:26.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.869][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:26.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.872][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.873][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:26.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:26.875][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.876][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.877][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:03:26.879][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.880][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:26.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.882][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:26.883][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.885][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.886][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.887][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:26.887][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:26.888][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.889][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:03:26.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:26.891][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.892][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.893][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:03:26.893][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:03:26.893][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:03:26.893][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:03:26.893][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:03:26.894][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:26.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.897][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:26.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.899][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.900][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.901][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:26.902][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:26.903][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.904][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.905][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:03:26.907][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.907][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:03:26.908][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.909][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:26.910][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.911][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.912][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.913][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.914][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:03:26.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:26.916][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.917][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:03:26.918][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:26.919][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.920][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.921][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.922][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:26.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.924][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:26.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.927][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.928][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.929][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:26.930][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:26.934][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.935][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.936][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:03:26.938][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.939][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:03:26.940][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.941][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:26.942][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.944][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.945][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:03:26.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:26.947][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.948][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:03:26.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:26.950][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.951][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:26.952][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.953][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:03:26.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.955][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.956][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:26.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:26.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:26.958][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:26.959][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.960][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:26.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:26.962][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:26.963][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:26.964][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:26.965][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.970][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[2025-12-06 16:03:26.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:26.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:26.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:26.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:26.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:26.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.034][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:03:27.035][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:03:27.041][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:03:27.042][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:03:27.043][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:03:27.045][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:03:27.046][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:27.047][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:27.048][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:03:27.050][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:03:27.051][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:03:27.052][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:03:27.054][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:03:27.055][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:03:27.056][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:03:27.058][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:03:27.059][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:03:27.060][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:03:27.062][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:03:27.063][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:03:27.064][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:03:27.066][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:03:27.067][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:03:27.068][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:03:27.070][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:03:27.071][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:03:27.072][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:03:27.073][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:03:27.075][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:03:27.076][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:03:27.077][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:03:27.079][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:03:27.080][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:03:27.081][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:03:27.083][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:03:27.084][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:03:27.085][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:03:27.086][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:03:27.088][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:03:27.089][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:03:27.090][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:03:27.092][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:03:27.093][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:03:27.094][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:03:27.096][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:03:27.097][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:03:27.098][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:03:27.100][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:03:27.101][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:03:27.102][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:03:27.103][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:03:27.105][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:03:27.106][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:03:27.107][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:03:27.109][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:03:27.110][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:03:27.111][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:03:27.113][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:03:27.114][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:03:27.115][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:03:27.117][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:03:27.118][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:03:27.119][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:03:27.120][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:03:27.122][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:03:27.123][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:03:27.124][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:03:27.126][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:03:27.127][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:03:27.128][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:03:27.130][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:03:27.131][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:03:27.132][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:03:27.134][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:03:27.135][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:03:27.136][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:03:27.138][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:03:27.139][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:03:27.140][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:03:27.146][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:03:27.147][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:03:27.149][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:03:27.150][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:03:27.151][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:03:27.153][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:03:27.154][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:03:27.155][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.156][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.157][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[2025-12-06 16:03:27.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.169][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[2025-12-06 16:03:27.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.192][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[2025-12-06 16:03:27.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.246][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[2025-12-06 16:03:27.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:03:27.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:03:27.257][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-06 16:03:27.258][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-06 16:03:27.260][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:27.261][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-06 16:03:27.262][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:27.263][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:03:27.264][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:27.265][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-06 16:03:27.266][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:27.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:03:27.268][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-06 16:03:27.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:03:27.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:27.270][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-06 16:03:27.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-06 16:03:27.272][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-06 16:03:27.273][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:03:27.274][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:27.275][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:03:27.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:27.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:27.278][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:03:27.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:03:27.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:03:27.280][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:03:27.281][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-06 16:03:27.281][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-06 16:03:27.281][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-06 16:03:27.281][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-06 16:03:27.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:03:27.283][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:03:27.284][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:03:27.285][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:03:27.286][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-06 16:03:27.289][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-06 16:03:27.292][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-06 16:03:27.293][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:03:27.294][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-06 16:03:27.295][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:03:27.296][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:03:27.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:03:27.297][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:03:27.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:03:27.299][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:03:27.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)