Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-17 23:55 -0500 (Sat, 17 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4886
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4676
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: 2026-01-17 09:55 -0500 (Sat, 17 Jan 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: 2026-01-17 16:01:42 -0500 (Sat, 17 Jan 2026)
EndedAt: 2026-01-17 16:03:03 -0500 (Sat, 17 Jan 2026)
EllapsedTime: 80.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-01-17 16:02:59.012][biodb::testContext]
biodb.INFO [2026-01-17 16:02:59.015][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:02:59.017][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-17 16:02:59.018][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:02:59.019][biodb::testContext]
biodb.INFO [2026-01-17 16:02:59.026][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:02:59.028][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-17 16:02:59.036][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:02:59.037][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-17 16:02:59.038][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.043][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-17 16:02:59.067][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.072][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-17 16:02:59.073][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.078][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-17 16:02:59.079][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-17 16:02:59.080][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-17 16:02:59.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.085][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-17 16:02:59.086][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-17 16:02:59.087][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.092][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-17 16:02:59.093][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-17 16:02:59.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.097][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-17 16:02:59.099][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-17 16:02:59.100][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-17 16:02:59.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.104][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-17 16:02:59.106][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.110][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-17 16:02:59.111][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-17 16:02:59.113][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-17 16:02:59.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.117][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:02:59.119][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-17 16:02:59.120][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-17 16:02:59.121][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-17 16:02:59.122][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-17 16:02:59.124][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-17 16:02:59.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.128][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-17 16:02:59.129][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-17 16:02:59.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.134][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-17 16:02:59.135][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-17 16:02:59.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.140][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-17 16:02:59.141][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-17 16:02:59.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.145][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-17 16:02:59.147][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-17 16:02:59.148][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-17 16:02:59.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.151][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[2026-01-17 16:02:59.153][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:02:59.154][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-17 16:02:59.164][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-17 16:02:59.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.169][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-17 16:02:59.171][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-17 16:02:59.172][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-17 16:02:59.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.179][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-17 16:02:59.223][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.250][self$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[2026-01-17 16:02:59.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:02:59.254][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.255][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.256][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.258][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:02:59.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:02:59.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.262][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-17 16:02:59.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:02:59.265][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.267][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:02:59.267][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:02:59.267][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:02:59.267][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:02:59.267][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:02:59.269][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:02:59.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:02:59.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.276][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.277][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.278][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:02:59.279][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:02:59.281][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.282][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.283][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-17 16:02:59.285][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.287][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:02:59.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:02:59.291][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.294][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.295][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:02:59.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:02:59.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.299][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-17 16:02:59.300][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:02:59.302][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.304][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:02:59.304][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:02:59.304][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:02:59.304][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:02:59.304][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:02:59.306][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:02:59.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:02:59.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.314][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:02:59.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:02:59.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.319][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.320][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-17 16:02:59.322][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.323][self$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[2026-01-17 16:02:59.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:02:59.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.330][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.332][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:02:59.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:02:59.335][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.336][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-17 16:02:59.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:02:59.338][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.340][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.341][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.342][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:02:59.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:02:59.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.350][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.351][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:02:59.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:02:59.354][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.355][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.356][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-17 16:02:59.359][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.360][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:02:59.361][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:02:59.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.369][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:02:59.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:02:59.371][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.372][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-17 16:02:59.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:02:59.375][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.376][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.377][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:02:59.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:02:59.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.387][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:02:59.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:02:59.390][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.392][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.395][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:02:59.397][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.398][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[2026-01-17 16:02:59.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.403][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[2026-01-17 16:02:59.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.409][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[2026-01-17 16:02:59.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.414][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[2026-01-17 16:02:59.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.420][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[2026-01-17 16:02:59.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.431][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[2026-01-17 16:02:59.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.493][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-17 16:02:59.498][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-17 16:02:59.500][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-17 16:02:59.501][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-17 16:02:59.503][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-17 16:02:59.505][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-17 16:02:59.507][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-17 16:02:59.508][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-17 16:02:59.510][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-17 16:02:59.512][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-17 16:02:59.514][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-17 16:02:59.515][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-17 16:02:59.517][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-17 16:02:59.519][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-17 16:02:59.521][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-17 16:02:59.522][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-17 16:02:59.524][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-17 16:02:59.526][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-17 16:02:59.527][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-17 16:02:59.529][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-17 16:02:59.531][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-17 16:02:59.532][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-17 16:02:59.534][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-17 16:02:59.536][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-17 16:02:59.538][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-17 16:02:59.539][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-17 16:02:59.541][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-17 16:02:59.543][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-17 16:02:59.544][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-17 16:02:59.546][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-17 16:02:59.548][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-17 16:02:59.550][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-17 16:02:59.551][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-17 16:02:59.553][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-17 16:02:59.555][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-17 16:02:59.556][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-17 16:02:59.558][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-17 16:02:59.560][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-17 16:02:59.561][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-17 16:02:59.563][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-17 16:02:59.565][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-17 16:02:59.566][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-17 16:02:59.568][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-17 16:02:59.570][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-17 16:02:59.572][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-17 16:02:59.573][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-17 16:02:59.575][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-17 16:02:59.577][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-17 16:02:59.578][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-17 16:02:59.580][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-17 16:02:59.582][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-17 16:02:59.584][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-17 16:02:59.585][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-17 16:02:59.587][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-17 16:02:59.589][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-17 16:02:59.590][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-17 16:02:59.592][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-17 16:02:59.594][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-17 16:02:59.596][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-17 16:02:59.597][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-17 16:02:59.599][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-17 16:02:59.601][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-17 16:02:59.602][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-17 16:02:59.604][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-17 16:02:59.606][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-17 16:02:59.607][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-17 16:02:59.609][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-17 16:02:59.611][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-17 16:02:59.613][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-17 16:02:59.614][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-17 16:02:59.616][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-17 16:02:59.618][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-17 16:02:59.619][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-17 16:02:59.621][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-17 16:02:59.623][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-17 16:02:59.624][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-17 16:02:59.626][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-17 16:02:59.628][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-17 16:02:59.630][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-17 16:02:59.631][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-17 16:02:59.633][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-17 16:02:59.635][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-17 16:02:59.636][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-17 16:02:59.644][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-17 16:02:59.646][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:02:59.649][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:02:59.650][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.652][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:02:59.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:02:59.791][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-17 16:02:59.804][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-17 16:02:59.806][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.808][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-17 16:02:59.809][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.810][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:02:59.812][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.813][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-17 16:02:59.814][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.817][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-17 16:02:59.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:02:59.819][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.821][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-17 16:02:59.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-17 16:02:59.823][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-17 16:02:59.825][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-17 16:02:59.826][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.827][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-17 16:02:59.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.831][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:02:59.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:02:59.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:02:59.835][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:02:59.836][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-17 16:02:59.836][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-17 16:02:59.836][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-17 16:02:59.836][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-17 16:02:59.837][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:02:59.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:02:59.839][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-17 16:02:59.841][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:02:59.849][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-17 16:02:59.870][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-17 16:02:59.887][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-17 16:02:59.898][biodb::testThat]
biodb.INFO [2026-01-17 16:02:59.900][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-17 16:02:59.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:02:59.902][biodb::testThat]
biodb.TRACE[2026-01-17 16:02:59.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-01-17 16:02:59.909][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-17 16:02:59.913][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-17 16:02:59.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-17 16:02:59.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:02:59.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:02:59.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:02:59.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:02:59.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:02:59.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-17 16:02:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:02:59.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:02:59.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:02:59.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:02:59.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:02:59.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:02:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:02:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:02:59.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:02:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:02:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:02:59.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-17 16:03:00.180][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-01-17 16:03:00.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:00.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.232][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.283][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.288][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.318][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.320][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.321][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.355][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.356][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.357][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.358][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.391][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.393][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.394][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.395][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.428][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.429][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.430][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.431][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.468][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.471][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.472][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.488][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.491][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.492][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.499][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.500][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.501][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.503][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.511][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.513][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.519][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.520][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.521][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.523][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.529][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.530][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.532][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.533][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.556][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-01-17 16:03:00.604][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-01-17 16:03:00.605][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-01-17 16:03:00.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-17 16:03:00.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:00.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:00.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:00.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:00.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:00.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-17 16:03:00.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:00.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.709][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:00.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:00.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.720][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:00.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:00.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:00.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:00.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:00.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:00.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.796][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.801][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.811][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-17 16:03:00.846][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-01-17 16:03:00.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.879][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:00.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:00.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.954][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.959][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.964][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-01-17 16:03:00.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:00.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:00.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:00.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:01.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:01.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.007][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:01.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:01.009][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.010][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:01.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:01.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.027][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.032][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.037][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.042][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.044][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.045][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.046][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.047][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.079][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.081][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.083][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.105][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.115][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.116][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.117][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.118][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.155][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.156][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.158][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.159][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.192][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.193][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.195][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.196][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.229][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.230][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.231][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.247][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:01.249][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:01.250][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.252][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.258][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.260][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:01.261][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.262][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.268][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:01.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:01.271][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.272][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:01.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:01.282][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.283][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.289][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.291][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:01.292][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.293][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.300][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.301][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-01-17 16:03:01.303][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.304][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:01.311][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:01.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:01.313][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:01.315][ef$get] fields variable is a list.
biodb.INFO [2026-01-17 16:03:01.326][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.328][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-17 16:03:01.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.330][biodb::testThat]
biodb.DEBUG[2026-01-17 16:03:01.333][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-01-17 16:03:01.337][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-01-17 16:03:01.340][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:01.385][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-17 16:03:01.387][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-17 16:03:01.388][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-17 16:03:01.606][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.607][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-17 16:03:01.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.609][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.618][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.619][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-17 16:03:01.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.621][biodb::testThat]
biodb.WARN [2026-01-17 16:03:01.643][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-01-17 16:03:01.670][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-01-17 16:03:01.682][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.683][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-17 16:03:01.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.686][biodb::testThat]
biodb.DEBUG[2026-01-17 16:03:01.710][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-01-17 16:03:01.775][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-17 16:03:01.777][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:01.778][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-01-17 16:03:01.780][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-01-17 16:03:01.801][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-01-17 16:03:01.873][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.874][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-17 16:03:01.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.877][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.887][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.888][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-17 16:03:01.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.891][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.901][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.902][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-17 16:03:01.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.905][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.913][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.914][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-17 16:03:01.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:01.917][biodb::testThat]
biodb.INFO [2026-01-17 16:03:01.925][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-17 16:03:01.927][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-17 16:03:01.928][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-17 16:03:01.929][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:01.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:01.931][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:01.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:01.934][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-01-17 16:03:01.948][biodb::testContext]
biodb.INFO [2026-01-17 16:03:01.949][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:03:01.950][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-01-17 16:03:01.951][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:03:01.953][biodb::testContext]
biodb.INFO [2026-01-17 16:03:01.955][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:03:01.957][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-17 16:03:01.961][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:01.963][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-17 16:03:01.964][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-17 16:03:01.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:01.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:01.968][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-17 16:03:01.970][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-17 16:03:01.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:01.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:01.974][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-17 16:03:01.975][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-17 16:03:01.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:01.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:01.980][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-17 16:03:01.986][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-17 16:03:01.987][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-17 16:03:01.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:01.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:01.992][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-17 16:03:01.993][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-17 16:03:01.994][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-17 16:03:01.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:01.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:01.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:01.999][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-17 16:03:02.000][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-17 16:03:02.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.005][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-17 16:03:02.006][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-17 16:03:02.007][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-17 16:03:02.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.012][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-17 16:03:02.013][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-17 16:03:02.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.018][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-17 16:03:02.019][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-17 16:03:02.020][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-17 16:03:02.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.025][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:03:02.026][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-17 16:03:02.027][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-17 16:03:02.028][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-17 16:03:02.030][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-17 16:03:02.031][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-17 16:03:02.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.036][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-17 16:03:02.037][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-17 16:03:02.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.041][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-17 16:03:02.043][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-17 16:03:02.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.047][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-17 16:03:02.049][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-17 16:03:02.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.053][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-17 16:03:02.054][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-17 16:03:02.056][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-17 16:03:02.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.060][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:03:02.062][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-17 16:03:02.073][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-17 16:03:02.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.077][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-17 16:03:02.078][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-17 16:03:02.080][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-17 16:03:02.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.084][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-17 16:03:02.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.088][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-17 16:03:02.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:02.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.096][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.097][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:03:02.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:02.100][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.101][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-17 16:03:02.102][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:02.103][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.105][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.106][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:03:02.106][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:03:02.106][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:03:02.106][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:03:02.106][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:03:02.107][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:02.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:02.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.116][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:02.118][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:02.119][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.121][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.122][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-17 16:03:02.125][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.126][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:03:02.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.129][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:02.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.133][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.136][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:03:02.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:02.138][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.140][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-17 16:03:02.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:02.142][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.143][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.145][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:03:02.145][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:03:02.145][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:03:02.145][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:03:02.145][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:03:02.146][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:02.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:02.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.153][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.155][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.156][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:02.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:02.158][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.159][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.161][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-17 16:03:02.163][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.165][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-17 16:03:02.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:02.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:03:02.175][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:02.177][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.178][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-17 16:03:02.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:02.181][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.182][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.183][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:02.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:02.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.197][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.198][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.199][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:02.200][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:02.202][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.203][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.204][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-17 16:03:02.207][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.208][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:03:02.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:02.211][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.216][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:03:02.218][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:02.219][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.220][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-17 16:03:02.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:02.223][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.225][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:02.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:02.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.232][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.234][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.235][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:02.237][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:02.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.240][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:02.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.244][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[2026-01-17 16:03:02.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.283][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[2026-01-17 16:03:02.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.335][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-17 16:03:02.337][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-17 16:03:02.339][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-17 16:03:02.340][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-17 16:03:02.342][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-17 16:03:02.344][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-17 16:03:02.345][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-17 16:03:02.347][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-17 16:03:02.349][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-17 16:03:02.350][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-17 16:03:02.352][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-17 16:03:02.354][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-17 16:03:02.356][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-17 16:03:02.357][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-17 16:03:02.359][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-17 16:03:02.361][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-17 16:03:02.363][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-17 16:03:02.364][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-17 16:03:02.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-17 16:03:02.368][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-17 16:03:02.370][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-17 16:03:02.371][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-17 16:03:02.373][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-17 16:03:02.375][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-17 16:03:02.376][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-17 16:03:02.378][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-17 16:03:02.380][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-17 16:03:02.382][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-17 16:03:02.388][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-17 16:03:02.389][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-17 16:03:02.391][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-17 16:03:02.393][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-17 16:03:02.394][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-17 16:03:02.396][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-17 16:03:02.398][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-17 16:03:02.399][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-17 16:03:02.401][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-17 16:03:02.403][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-17 16:03:02.405][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-17 16:03:02.406][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-17 16:03:02.408][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-17 16:03:02.410][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-17 16:03:02.411][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-17 16:03:02.413][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-17 16:03:02.415][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-17 16:03:02.416][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-17 16:03:02.418][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-17 16:03:02.420][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-17 16:03:02.422][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-17 16:03:02.423][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-17 16:03:02.425][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-17 16:03:02.427][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-17 16:03:02.429][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-17 16:03:02.430][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-17 16:03:02.432][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-17 16:03:02.434][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-17 16:03:02.436][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-17 16:03:02.437][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-17 16:03:02.439][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-17 16:03:02.441][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-17 16:03:02.442][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-17 16:03:02.444][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-17 16:03:02.446][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-17 16:03:02.448][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-17 16:03:02.449][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-17 16:03:02.451][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-17 16:03:02.453][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-17 16:03:02.455][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-17 16:03:02.456][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-17 16:03:02.458][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-17 16:03:02.460][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-17 16:03:02.461][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-17 16:03:02.463][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-17 16:03:02.465][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-17 16:03:02.466][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-17 16:03:02.468][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-17 16:03:02.470][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-17 16:03:02.472][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-17 16:03:02.473][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-17 16:03:02.475][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-17 16:03:02.477][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-17 16:03:02.478][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-17 16:03:02.480][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-17 16:03:02.483][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-17 16:03:02.485][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:03:02.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:02.489][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.492][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.619][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[2026-01-17 16:03:02.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:02.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:02.644][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-01-17 16:03:02.646][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-01-17 16:03:02.648][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.649][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-01-17 16:03:02.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:02.653][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.654][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-01-17 16:03:02.656][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.658][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-01-17 16:03:02.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:02.660][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.662][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-01-17 16:03:02.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-01-17 16:03:02.664][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-01-17 16:03:02.665][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:02.667][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.668][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-17 16:03:02.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.671][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:02.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:02.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:02.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:02.676][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-17 16:03:02.676][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-01-17 16:03:02.676][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-01-17 16:03:02.676][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-01-17 16:03:02.677][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:02.678][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:02.680][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:02.681][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:02.682][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-01-17 16:03:02.686][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-01-17 16:03:02.690][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-01-17 16:03:02.692][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-17 16:03:02.693][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-01-17 16:03:02.694][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-17 16:03:02.695][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:02.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:02.697][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:02.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:02.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:02.701][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".
[ 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)