Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-20 23:55 -0500 (Sat, 20 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
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: 2025-12-20 09:55 -0500 (Sat, 20 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: 2025-12-20 16:02:27 -0500 (Sat, 20 Dec 2025)
EndedAt: 2025-12-20 16:03:31 -0500 (Sat, 20 Dec 2025)
EllapsedTime: 64.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-12-20 16:03:27.709][biodb::testContext]
biodb.INFO [2025-12-20 16:03:27.711][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:03:27.712][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-20 16:03:27.713][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:03:27.714][biodb::testContext]
biodb.INFO [2025-12-20 16:03:27.720][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:03:27.722][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:03:27.729][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:27.730][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:03:27.731][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.734][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:03:27.751][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.755][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:03:27.756][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.768][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:03:27.769][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:03:27.770][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:03:27.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.773][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:03:27.774][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:03:27.775][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.778][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:03:27.779][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:03:27.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.783][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:03:27.784][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:03:27.785][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:03:27.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.788][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:03:27.789][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.792][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:03:27.793][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:03:27.794][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:03:27.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.797][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:03:27.798][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:03:27.799][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:03:27.800][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:03:27.801][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:03:27.802][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:03:27.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.805][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:03:27.806][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:03:27.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.810][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:03:27.811][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:03:27.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.814][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:03:27.815][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:03:27.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.818][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:03:27.819][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:03:27.820][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:03:27.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.824][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:03:27.825][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:03:27.829][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:03:27.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.833][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:03:27.833][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:03:27.834][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:03:27.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:27.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:27.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:27.840][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:03:27.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.886][self$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[2025-12-20 16:03:27.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:27.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.890][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.891][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.892][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:03:27.893][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:27.894][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.895][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:03:27.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:27.897][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.898][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.899][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:03:27.899][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:03:27.899][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:03:27.899][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:03:27.899][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:03:27.900][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:27.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.902][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:27.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.906][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:27.908][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:27.909][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.910][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.911][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:03:27.912][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.913][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:03:27.914][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.915][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:27.916][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.917][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.918][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.919][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.924][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:03:27.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:27.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.927][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:03:27.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:27.929][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.930][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.931][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:03:27.931][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:03:27.931][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:03:27.931][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:03:27.931][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:03:27.932][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:27.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:27.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.938][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:27.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:27.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.941][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.943][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:03:27.944][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.945][self$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[2025-12-20 16:03:27.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:27.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.950][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.952][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:03:27.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:27.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.954][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:03:27.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:27.956][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.958][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:27.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.962][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:27.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.965][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.966][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:27.967][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:27.968][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.969][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.970][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:03:27.971][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.972][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:03:27.973][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:27.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.977][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.978][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.979][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:03:27.980][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:27.981][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.982][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:03:27.983][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:27.983][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.984][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:27.985][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.986][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:27.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.989][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:27.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:27.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:27.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:27.992][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:27.993][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:27.994][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:27.995][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:27.996][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:28.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:28.000][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.068][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:03:28.073][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:03:28.074][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:03:28.075][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:03:28.077][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:03:28.106][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:03:28.108][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:03:28.110][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:03:28.111][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:03:28.113][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:03:28.114][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:03:28.116][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:03:28.117][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:03:28.119][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:03:28.120][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:03:28.122][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:03:28.124][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:03:28.125][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:03:28.127][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:03:28.128][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:03:28.130][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:03:28.131][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:03:28.133][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:03:28.134][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:03:28.136][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:03:28.137][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:03:28.138][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:03:28.140][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:03:28.141][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:03:28.143][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:03:28.144][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:03:28.146][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:03:28.147][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:03:28.148][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:03:28.150][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:03:28.151][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:03:28.153][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:03:28.154][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:03:28.156][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:03:28.157][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:03:28.158][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:03:28.160][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:03:28.161][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:03:28.163][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:03:28.164][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:03:28.165][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:03:28.167][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:03:28.168][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:03:28.170][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:03:28.171][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:03:28.173][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:03:28.174][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:03:28.175][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:03:28.177][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:03:28.178][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:03:28.180][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:03:28.181][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:03:28.182][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:03:28.184][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:03:28.185][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:03:28.187][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:03:28.188][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:03:28.189][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:03:28.191][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:03:28.192][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:03:28.194][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:03:28.195][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:03:28.196][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:03:28.198][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:03:28.199][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:03:28.201][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:03:28.202][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:03:28.203][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:03:28.205][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:03:28.206][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:03:28.208][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:03:28.209][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:03:28.211][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:03:28.212][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:03:28.213][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:03:28.215][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:03:28.216][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:03:28.218][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:03:28.224][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:03:28.226][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:03:28.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:28.230][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.232][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:28.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:28.338][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-20 16:03:28.347][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-20 16:03:28.349][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:28.350][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-20 16:03:28.351][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:28.352][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:28.353][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:28.354][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-20 16:03:28.355][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:28.356][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:28.357][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-20 16:03:28.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:28.359][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:28.360][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-20 16:03:28.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-20 16:03:28.361][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-20 16:03:28.362][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:28.363][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:28.364][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:03:28.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:28.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:28.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:28.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:28.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:28.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:28.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-20 16:03:28.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-20 16:03:28.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-20 16:03:28.370][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-20 16:03:28.371][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:28.372][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:28.373][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:28.374][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:28.380][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-20 16:03:28.400][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-20 16:03:28.415][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-20 16:03:28.423][biodb::testThat]
biodb.INFO [2025-12-20 16:03:28.424][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:03:28.425][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:28.426][biodb::testThat]
biodb.TRACE[2025-12-20 16:03:28.429][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-12-20 16:03:28.430][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:03:28.434][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-20 16:03:28.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:03:28.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:03:28.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.565][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:03:28.626][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-12-20 16:03:28.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:03:28.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:03:28.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.632][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:03:28.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:03:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:03:28.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:03:28.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:03:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:03:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.731][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:28.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.759][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.760][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.762][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.773][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.784][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.785][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.787][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.809][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.810][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.812][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.835][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.836][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.837][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.864][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.867][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.878][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.881][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.885][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:28.885][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:28.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.887][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.891][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:28.892][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:28.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.894][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.898][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.899][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:28.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.900][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.904][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.905][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:28.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.907][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.923][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-12-20 16:03:28.959][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:03:28.961][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-12-20 16:03:28.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:03:28.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:28.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:28.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:28.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:28.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:28.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:03:28.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:28.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:28.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:28.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.008][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.054][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.073][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:03:29.111][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-12-20 16:03:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:03:29.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:03:29.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:03:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:03:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.137][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:03:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:03:29.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:03:29.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:03:29.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.152][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-12-20 16:03:29.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.223][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.224][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.226][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.237][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.249][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.249][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.251][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.274][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.274][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.276][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.298][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.299][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.301][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.327][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.328][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.330][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.353][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.355][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.377][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.378][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.380][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.391][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:03:29.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:03:29.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.394][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.398][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.399][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:03:29.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.400][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.404][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:03:29.405][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:03:29.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.407][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:03:29.412][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:03:29.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.414][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:03:29.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.420][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.428][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.429][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:03:29.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.431][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:03:29.434][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:03:29.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:03:29.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:03:29.437][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:03:29.443][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.444][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:03:29.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.446][biodb::testThat]
biodb.DEBUG[2025-12-20 16:03:29.448][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-12-20 16:03:29.450][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-12-20 16:03:29.453][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-20 16:03:29.480][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-20 16:03:29.481][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-20 16:03:29.482][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-20 16:03:29.610][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.611][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:03:29.612][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.613][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.618][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.619][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:03:29.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.621][biodb::testThat]
biodb.WARN [2025-12-20 16:03:29.643][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-20 16:03:29.661][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-20 16:03:29.668][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.669][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:03:29.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.671][biodb::testThat]
biodb.DEBUG[2025-12-20 16:03:29.687][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-12-20 16:03:29.734][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:03:29.735][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-12-20 16:03:29.736][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-12-20 16:03:29.738][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-12-20 16:03:29.749][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2025-12-20 16:03:29.799][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.800][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:03:29.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.802][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.809][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.810][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:03:29.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.812][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.822][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.823][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:03:29.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.824][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.830][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.830][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:03:29.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:03:29.832][biodb::testThat]
biodb.INFO [2025-12-20 16:03:29.837][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:03:29.838][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-20 16:03:29.839][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:03:29.840][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:29.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:29.842][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:29.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:29.843][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-20 16:03:29.853][biodb::testContext]
biodb.INFO [2025-12-20 16:03:29.854][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:03:29.855][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-12-20 16:03:29.856][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:03:29.856][biodb::testContext]
biodb.INFO [2025-12-20 16:03:29.858][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:03:29.860][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:03:29.863][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:29.864][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:03:29.865][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.869][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:03:29.869][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.873][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:03:29.874][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.877][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:03:29.878][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:03:29.879][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:03:29.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.882][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:03:29.883][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:03:29.884][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.888][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:03:29.889][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:03:29.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.892][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:03:29.893][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:03:29.894][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:03:29.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.896][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[2025-12-20 16:03:29.897][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:03:29.898][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.902][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:03:29.903][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:03:29.903][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:03:29.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.907][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:03:29.908][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:03:29.909][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:03:29.910][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:03:29.911][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:03:29.912][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:03:29.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.915][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:03:29.916][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:03:29.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.919][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:03:29.920][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:03:29.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.928][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:03:29.929][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:03:29.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.932][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:03:29.933][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:03:29.934][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:03:29.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.937][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:03:29.938][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:03:29.943][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:03:29.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.945][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[2025-12-20 16:03:29.946][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:03:29.947][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:03:29.948][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:03:29.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:29.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:29.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:29.952][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:03:29.953][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:29.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-20 16:03:29.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:29.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:29.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:29.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:29.961][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:03:29.962][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:29.963][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.964][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:03:29.965][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:29.966][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:29.966][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.967][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:03:29.967][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:03:29.967][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:03:29.967][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:03:29.967][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:03:29.968][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:29.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:29.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:29.971][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:29.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:29.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:29.974][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:29.975][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:29.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:29.976][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:29.977][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:29.978][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:29.979][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:03:29.981][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:29.982][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:03:29.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:29.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:29.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:29.987][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:29.988][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:03:29.989][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:29.990][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.991][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:03:29.992][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:29.993][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:29.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:29.995][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:03:29.995][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:03:29.995][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:03:29.995][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:03:29.995][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:03:29.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:29.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:29.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:29.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:29.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.001][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.002][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.003][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:30.004][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:30.005][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.006][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.007][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:03:30.008][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.009][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-20 16:03:30.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:30.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.013][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.015][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.016][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:03:30.017][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:30.018][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.019][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:03:30.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:30.021][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.022][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:30.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.026][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:30.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.030][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:30.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:30.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.037][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.038][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:03:30.040][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.041][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:03:30.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:30.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.045][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.047][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:03:30.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:30.049][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.050][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:03:30.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:30.052][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.053][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.054][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:03:30.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:30.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.060][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.061][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:30.063][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:30.064][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.064][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.066][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:30.066][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.135][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:03:30.136][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:03:30.141][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:03:30.142][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:03:30.144][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:03:30.145][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:03:30.146][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:03:30.147][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:03:30.149][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:03:30.150][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:03:30.151][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:03:30.153][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:03:30.154][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:03:30.155][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:03:30.156][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:03:30.158][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:03:30.159][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:03:30.160][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:03:30.162][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:03:30.163][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:03:30.164][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:03:30.165][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:03:30.167][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:03:30.168][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:03:30.169][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:03:30.171][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:03:30.172][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:03:30.173][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:03:30.174][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:03:30.176][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:03:30.177][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:03:30.178][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:03:30.180][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:03:30.181][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:03:30.182][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:03:30.183][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:03:30.185][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:03:30.186][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:03:30.187][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:03:30.188][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:03:30.190][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:03:30.191][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:03:30.192][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:03:30.194][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:03:30.195][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:03:30.196][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:03:30.197][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:03:30.199][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:03:30.200][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:03:30.201][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:03:30.203][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:03:30.204][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:03:30.205][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:03:30.206][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:03:30.208][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:03:30.209][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:03:30.210][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:03:30.212][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:03:30.213][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:03:30.214][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:03:30.215][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:03:30.217][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:03:30.218][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:03:30.219][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:03:30.221][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:03:30.222][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:03:30.223][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:03:30.224][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:03:30.226][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:03:30.227][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:03:30.228][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:03:30.230][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:03:30.231][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:03:30.232][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:03:30.234][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:03:30.235][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:03:30.236][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:03:30.237][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:03:30.243][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:03:30.244][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:03:30.245][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:03:30.247][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:03:30.248][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:03:30.249][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:03:30.251][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:03:30.252][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:03:30.252][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.254][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.255][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[2025-12-20 16:03:30.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.342][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.DEBUG[2025-12-20 16:03:30.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:03:30.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:03:30.353][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-12-20 16:03:30.354][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-12-20 16:03:30.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.357][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-12-20 16:03:30.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.359][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:03:30.360][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.361][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-12-20 16:03:30.362][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.364][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-12-20 16:03:30.365][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:03:30.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.366][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-12-20 16:03:30.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-12-20 16:03:30.368][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-12-20 16:03:30.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:03:30.370][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.371][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:03:30.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:03:30.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:03:30.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:03:30.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:03:30.377][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-20 16:03:30.377][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-12-20 16:03:30.377][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-12-20 16:03:30.377][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-12-20 16:03:30.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:03:30.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:03:30.380][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:03:30.381][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:03:30.382][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-12-20 16:03:30.385][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-12-20 16:03:30.388][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-12-20 16:03:30.389][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:03:30.390][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-12-20 16:03:30.391][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:03:30.392][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:03:30.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:03:30.393][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:03:30.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:03:30.395][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:03:30.396][FUN] Functions in observer 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)