Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-07 23:55 -0500 (Sat, 07 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4684
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-07 09:55 -0500 (Sat, 07 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -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 merida1

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-03-07 16:01:50 -0500 (Sat, 07 Mar 2026)
EndedAt: 2026-03-07 16:03:12 -0500 (Sat, 07 Mar 2026)
EllapsedTime: 81.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-03-07 16:03:08.186][biodb::testContext]
biodb.INFO [2026-03-07 16:03:08.189][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:08.191][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-07 16:03:08.192][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:08.193][biodb::testContext]
biodb.INFO [2026-03-07 16:03:08.200][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:08.202][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:08.210][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:08.211][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:03:08.212][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.217][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:03:08.241][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.245][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:03:08.247][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.251][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:03:08.253][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:03:08.254][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:03:08.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.258][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:03:08.260][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:03:08.261][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.266][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:03:08.267][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:03:08.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.271][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:03:08.273][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:03:08.274][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:03:08.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.279][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:03:08.280][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.285][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:03:08.286][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:03:08.287][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:03:08.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.292][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:08.293][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:03:08.294][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:03:08.295][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:03:08.297][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:03:08.298][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:03:08.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.302][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[2026-03-07 16:03:08.303][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:03:08.304][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:03:08.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.309][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:03:08.310][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:03:08.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.315][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:03:08.316][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:03:08.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.321][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:03:08.322][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:03:08.323][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:03:08.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.328][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:08.329][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:03:08.340][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:03:08.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.345][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:03:08.346][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:03:08.348][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:03:08.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.355][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:03:08.400][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.429][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:03:08.430][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.431][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:08.433][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.435][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.438][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:08.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:08.440][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.441][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:03:08.443][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:08.444][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.445][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.446][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:08.446][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:08.446][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:08.446][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:08.446][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:08.448][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:08.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.451][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:08.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.455][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.456][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:08.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:08.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.461][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.462][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:03:08.464][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.466][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:08.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:08.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.473][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.474][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:08.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:08.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.478][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:03:08.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:08.481][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:08.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:08.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:08.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:08.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:08.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:08.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.488][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:08.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.493][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:08.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:08.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.498][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.499][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:03:08.501][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.503][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:03:08.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:08.507][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.511][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.512][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:08.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:08.514][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.516][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:03:08.517][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:08.518][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.519][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.521][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.522][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:08.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.526][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:08.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.529][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.530][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.532][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:08.533][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:08.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.535][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.537][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:03:08.539][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.540][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:08.542][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.543][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:08.544][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.549][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:08.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:08.552][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.553][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:03:08.555][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:08.556][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.558][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:08.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.563][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:08.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:08.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:08.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:08.568][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:08.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:08.572][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.573][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:08.577][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:08.579][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.670][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:03:08.675][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:03:08.677][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:03:08.683][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:03:08.685][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:03:08.686][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:03:08.688][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:08.690][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:08.692][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:03:08.694][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:03:08.696][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:03:08.697][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:03:08.699][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:08.701][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:08.702][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:03:08.704][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:03:08.706][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:03:08.708][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:03:08.709][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:03:08.711][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:03:08.713][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:03:08.714][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:03:08.716][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:03:08.718][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:03:08.720][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:03:08.722][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:03:08.723][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:03:08.725][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:03:08.727][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:03:08.729][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:03:08.730][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:03:08.732][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:03:08.734][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:03:08.736][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:03:08.738][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:03:08.739][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:03:08.741][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:03:08.743][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:03:08.745][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:03:08.746][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:03:08.748][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:03:08.750][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:03:08.752][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:03:08.753][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:03:08.755][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:03:08.757][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:03:08.758][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:03:08.760][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:03:08.762][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:03:08.764][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:03:08.765][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:03:08.767][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:03:08.769][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:03:08.770][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:03:08.772][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:03:08.774][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:03:08.776][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:03:08.777][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:03:08.779][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:03:08.781][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:03:08.782][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:03:08.784][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:03:08.786][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:03:08.788][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:03:08.789][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:03:08.791][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:03:08.793][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:03:08.794][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:03:08.796][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:03:08.798][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:03:08.799][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:03:08.801][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:03:08.803][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:03:08.804][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:03:08.806][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:03:08.808][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:03:08.810][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:03:08.811][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:03:08.813][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:03:08.815][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:03:08.816][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:03:08.818][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:03:08.820][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:03:08.827][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:03:08.829][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:08.833][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:08.834][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.837][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[2026-03-07 16:03:08.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:08.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:08.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:08.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:08.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:08.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:08.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:08.971][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.DEBUG[2026-03-07 16:03:08.974][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:08.987][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-07 16:03:08.989][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.991][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-07 16:03:08.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:08.995][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:08.996][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-07 16:03:08.997][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:08.998][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:09.000][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-07 16:03:09.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:09.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:09.004][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-07 16:03:09.005][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-07 16:03:09.006][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-07 16:03:09.008][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:09.009][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:09.010][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:03:09.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:09.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:09.014][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:09.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:09.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:09.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:09.018][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:09.018][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:09.018][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-07 16:03:09.018][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-07 16:03:09.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:09.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:09.022][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:09.023][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:09.031][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-07 16:03:09.054][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-07 16:03:09.072][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-07 16:03:09.082][biodb::testThat]
biodb.INFO [2026-03-07 16:03:09.083][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:03:09.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:09.086][biodb::testThat]
biodb.TRACE[2026-03-07 16:03:09.090][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-03-07 16:03:09.093][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:03:09.096][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-07 16:03:09.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:03:09.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:09.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:09.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:09.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:09.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:09.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:03:09.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.268][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.273][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.283][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:03:09.363][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-03-07 16:03:09.366][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.371][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:09.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:09.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.376][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:09.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:09.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.382][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:09.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.411][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.460][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.465][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.470][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.500][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.503][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.504][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.537][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.540][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.541][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.573][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.575][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.576][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.577][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.609][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.610][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.612][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.613][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.647][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.649][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.670][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.671][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.673][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.674][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.680][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.682][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.683][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.684][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.690][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.692][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.693][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.694][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.703][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.704][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.711][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.712][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.713][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.714][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.737][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-03-07 16:03:09.784][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:03:09.786][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-07 16:03:09.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:03:09.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:09.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:09.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:09.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:09.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:09.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-07 16:03:09.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.850][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:09.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:09.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.855][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:09.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.861][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:09.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:09.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:09.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:09.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:09.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:09.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:09.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.974][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.979][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.989][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:09.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:09.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:09.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:09.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:09.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:03:10.025][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-03-07 16:03:10.052][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:10.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:10.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.058][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:10.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:10.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:10.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:10.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:10.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.138][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.143][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-07 16:03:10.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.185][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.188][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.189][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.206][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.216][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.221][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.223][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.224][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.225][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.259][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.261][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.262][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.264][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.290][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.300][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.302][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.303][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.304][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.337][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.339][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.341][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.377][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.379][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.380][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.381][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.413][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.415][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.416][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.417][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.434][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:10.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:10.437][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.438][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.445][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.446][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:10.447][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.448][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.455][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:10.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:10.457][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.459][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:10.466][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:10.468][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.469][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.475][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.477][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:10.478][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.479][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.486][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.487][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-07 16:03:10.488][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.489][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:10.496][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:10.497][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:10.498][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:10.500][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:03:10.510][biodb::testThat]
biodb.INFO [2026-03-07 16:03:10.511][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:03:10.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:10.514][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:10.516][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-03-07 16:03:10.521][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-03-07 16:03:10.524][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:10.564][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-07 16:03:10.566][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-07 16:03:10.567][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-07 16:03:10.745][biodb::testThat]
biodb.INFO [2026-03-07 16:03:10.746][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:03:10.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:10.749][biodb::testThat]
biodb.INFO [2026-03-07 16:03:10.757][biodb::testThat]
biodb.INFO [2026-03-07 16:03:10.758][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:03:10.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:10.761][biodb::testThat]
biodb.WARN [2026-03-07 16:03:10.790][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-07 16:03:10.815][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-07 16:03:10.826][biodb::testThat]
biodb.INFO [2026-03-07 16:03:10.827][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:03:10.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:10.829][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:10.852][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-03-07 16:03:10.915][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:03:10.917][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:10.919][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-07 16:03:10.920][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-07 16:03:10.938][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-07 16:03:11.014][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.016][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:03:11.017][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:11.018][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.028][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.029][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:03:11.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:11.031][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.041][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.043][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:11.044][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:11.045][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.054][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.055][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:11.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:11.057][biodb::testThat]
biodb.INFO [2026-03-07 16:03:11.065][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:03:11.067][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-07 16:03:11.068][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:03:11.069][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.071][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.073][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-07 16:03:11.087][biodb::testContext]
biodb.INFO [2026-03-07 16:03:11.089][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:11.090][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-03-07 16:03:11.091][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:11.092][biodb::testContext]
biodb.INFO [2026-03-07 16:03:11.095][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:11.097][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:11.101][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:11.103][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:03:11.104][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.109][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:03:11.110][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.114][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:03:11.116][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.120][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:03:11.122][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:03:11.123][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:03:11.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.127][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:03:11.129][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:03:11.130][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.134][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:03:11.135][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:03:11.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.140][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:03:11.141][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:03:11.142][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:03:11.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.147][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:03:11.148][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.152][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:03:11.154][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:03:11.155][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:03:11.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.164][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:11.165][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:03:11.166][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:03:11.168][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:03:11.169][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:03:11.170][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:03:11.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.174][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:03:11.176][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:03:11.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.180][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:03:11.181][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:03:11.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.186][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:03:11.187][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:03:11.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.191][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:03:11.192][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:03:11.194][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:03:11.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.198][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:11.199][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:03:11.209][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:03:11.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.214][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:03:11.215][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:03:11.216][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:03:11.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.221][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:03:11.223][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.224][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-07 16:03:11.226][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.227][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:11.228][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.229][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.230][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.233][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:11.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:11.235][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.236][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:03:11.238][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:11.239][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.240][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.241][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:11.241][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:11.241][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:11.241][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:11.241][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:11.243][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:11.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.246][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:11.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.248][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.249][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.251][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.252][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:11.253][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:11.254][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.255][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.257][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:03:11.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.260][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:11.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:11.264][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.266][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.268][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:11.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:11.271][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.272][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:03:11.273][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:11.274][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.277][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:11.277][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:11.277][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:11.277][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:11.277][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:11.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:11.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:11.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.286][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:11.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:11.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.292][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:03:11.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.296][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-07 16:03:11.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:11.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.301][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.304][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:11.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:11.307][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.308][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:03:11.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:11.310][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.313][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:11.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:11.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.322][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:11.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:11.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.327][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.328][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:03:11.331][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.332][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:11.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.334][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:11.336][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.337][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.338][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.340][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:11.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:11.343][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.344][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:03:11.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:11.347][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.348][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.349][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.350][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:11.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:11.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.357][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.359][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:11.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:11.366][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.367][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.369][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:11.370][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.459][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:03:11.461][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:03:11.462][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:03:11.464][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:03:11.466][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:03:11.467][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:03:11.469][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:11.471][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:11.472][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:03:11.474][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:03:11.476][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:03:11.477][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:03:11.479][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:11.480][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:11.482][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:03:11.484][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:03:11.485][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:03:11.487][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:03:11.489][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:03:11.490][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:03:11.492][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:03:11.494][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:03:11.495][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:03:11.497][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:03:11.499][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:03:11.500][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:03:11.502][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:03:11.504][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:03:11.505][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:03:11.507][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:03:11.509][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:03:11.511][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:03:11.512][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:03:11.514][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:03:11.516][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:03:11.517][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:03:11.519][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:03:11.520][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:03:11.522][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:03:11.524][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:03:11.526][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:03:11.527][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:03:11.529][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:03:11.531][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:03:11.532][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:03:11.534][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:03:11.536][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:03:11.537][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:03:11.539][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:03:11.541][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:03:11.542][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:03:11.544][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:03:11.550][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:03:11.552][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:03:11.554][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:03:11.555][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:03:11.557][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:03:11.558][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:03:11.560][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:03:11.562][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:03:11.563][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:03:11.565][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:03:11.567][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:03:11.568][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:03:11.570][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:03:11.572][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:03:11.573][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:03:11.575][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:03:11.577][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:03:11.578][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:03:11.580][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:03:11.582][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:03:11.583][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:03:11.585][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:03:11.587][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:03:11.588][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:03:11.590][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:03:11.592][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:03:11.593][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:03:11.595][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:03:11.597][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:03:11.598][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:03:11.600][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:03:11.602][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:03:11.604][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:11.605][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:11.606][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.608][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:11.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:11.737][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:11.750][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-07 16:03:11.752][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.753][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-07 16:03:11.755][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:11.757][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.758][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-07 16:03:11.759][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.761][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.762][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-07 16:03:11.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:11.764][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.766][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-07 16:03:11.767][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-07 16:03:11.768][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-07 16:03:11.769][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:11.771][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.772][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:03:11.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:11.776][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:11.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:11.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:11.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:11.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-07 16:03:11.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-07 16:03:11.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-07 16:03:11.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:11.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:11.783][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:11.785][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:11.786][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-07 16:03:11.790][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-07 16:03:11.794][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-07 16:03:11.795][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:03:11.797][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-07 16:03:11.798][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:03:11.799][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:11.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:11.801][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:11.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:11.803][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:11.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbNci.Rcheck/00install.out

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