Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-09 23:55 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
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 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-09 09:55 -0400 (Sat, 09 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-08-09 16:02:36 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 16:03:34 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 58.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-08-09 16:03:31.144][biodb::testContext]
biodb.INFO [2025-08-09 16:03:31.146][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:31.147][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-09 16:03:31.147][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:31.148][biodb::testContext]
biodb.INFO [2025-08-09 16:03:31.154][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:31.156][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:31.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:31.163][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:31.164][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.168][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:31.185][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.188][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:31.189][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.192][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:31.193][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:31.194][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:31.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.198][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:31.199][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:31.200][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.203][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:31.204][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:31.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.207][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:31.208][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:31.209][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:31.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.213][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:31.214][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.217][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:31.218][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:31.219][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:31.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.222][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:31.223][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:31.224][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:31.225][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:31.226][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:31.227][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:31.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.230][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:31.231][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:31.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.235][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:31.236][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:31.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.239][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:31.240][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:31.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.243][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:31.244][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:31.245][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:31.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.249][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:31.250][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:31.255][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:31.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.258][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:31.259][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:31.260][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:31.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.271][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:31.301][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.316][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:31.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:31.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.320][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.321][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.322][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.323][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:31.324][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:31.325][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.326][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:31.327][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:31.328][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:31.329][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:31.330][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:31.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:31.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.336][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.337][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:31.338][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:31.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.340][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.341][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:31.343][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.344][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:31.345][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:31.347][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.351][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:31.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:31.353][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.354][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:31.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:31.355][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.356][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.357][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:31.357][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:31.357][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:31.357][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:31.357][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:31.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:31.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:31.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.365][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.365][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:31.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:31.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.368][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.369][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:31.371][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.372][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-09 16:03:31.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:31.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.378][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:31.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:31.380][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.381][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:31.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:31.383][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.384][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.385][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.386][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:31.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:31.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.392][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:31.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:31.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.395][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.396][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:31.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.399][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:31.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:31.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.405][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:31.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:31.407][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.408][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:31.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:31.410][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.412][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.413][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:31.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.415][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:31.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.418][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.419][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:31.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:31.422][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.423][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.430][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:31.431][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.453][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[2025-08-09 16:03:31.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.465][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[2025-08-09 16:03:31.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.494][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[2025-08-09 16:03:31.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.499][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:31.503][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:31.505][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:31.506][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:31.507][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:31.509][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:31.510][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:31.511][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:31.513][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:31.514][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:31.515][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:31.516][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:31.518][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:31.519][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:31.520][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:31.522][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:31.523][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:31.524][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:31.525][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:31.527][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:31.528][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:31.529][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:31.531][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:31.532][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:31.533][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:31.534][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:31.536][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:31.537][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:31.538][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:31.540][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:31.541][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:31.542][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:31.544][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:31.545][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:31.546][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:31.547][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:31.549][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:31.550][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:31.551][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:31.552][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:31.554][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:31.555][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:31.556][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:31.558][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:31.559][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:31.560][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:31.562][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:31.563][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:31.564][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:31.565][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:31.567][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:31.568][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:31.569][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:31.571][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:31.572][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:31.573][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:31.574][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:31.576][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:31.577][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:31.578][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:31.580][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:31.581][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:31.582][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:31.583][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:31.585][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:31.586][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:31.587][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:31.589][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:31.594][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:31.595][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:31.596][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:31.598][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:31.599][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:31.600][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:31.601][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:31.603][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:31.604][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:31.605][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:31.607][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:31.608][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:31.609][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:31.610][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:31.612][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:31.617][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:31.619][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:31.622][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:31.622][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.624][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.675][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[2025-08-09 16:03:31.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:31.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:31.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.721][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[2025-08-09 16:03:31.723][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:31.739][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-09 16:03:31.742][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.743][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-09 16:03:31.744][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.745][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:31.747][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.748][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-09 16:03:31.749][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.750][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.751][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-09 16:03:31.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:31.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.754][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-09 16:03:31.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-09 16:03:31.756][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-09 16:03:31.757][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:31.772][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.773][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:31.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.775][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:31.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:31.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:31.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:31.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:31.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:31.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-09 16:03:31.780][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-09 16:03:31.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:31.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:31.783][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:31.784][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:31.790][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-09 16:03:31.812][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-09 16:03:31.828][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-09 16:03:31.837][biodb::testThat]
biodb.INFO [2025-08-09 16:03:31.838][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-09 16:03:31.839][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:31.840][biodb::testThat]
biodb.TRACE[2025-08-09 16:03:31.843][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-08-09 16:03:31.845][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:31.848][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-09 16:03:31.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:31.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:31.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:31.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:31.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:31.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:31.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:31.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:31.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:31.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:31.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.913][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:31.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:31.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:31.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:31.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:31.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:31.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:31.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:31.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:31.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:31.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:31.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:31.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:31.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:31.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:31.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:31.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.980][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.984][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:31.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:31.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:31.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:31.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:31.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:31.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:31.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:32.047][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-08-09 16:03:32.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:32.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:32.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:32.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:32.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.115][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.119][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.143][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.144][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.145][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.168][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.169][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.192][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.195][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.223][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.259][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.260][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.262][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.266][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.267][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.272][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.273][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.275][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.281][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.285][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.286][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.288][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.303][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-08-09 16:03:32.370][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-09 16:03:32.371][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-09 16:03:32.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-09 16:03:32.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:32.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:32.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:32.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:32.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:32.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-09 16:03:32.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.414][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.481][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.484][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.495][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-09 16:03:32.521][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-08-09 16:03:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-09 16:03:32.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-09 16:03:32.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:32.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-09 16:03:32.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.563][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.597][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.600][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-09 16:03:32.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.633][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.634][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.636][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.647][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.650][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.654][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.658][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.659][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.661][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.661][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.683][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.684][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.685][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.707][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.708][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.732][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.733][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.735][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.761][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.785][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.786][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.799][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-09 16:03:32.800][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-09 16:03:32.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.802][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.805][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.806][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-09 16:03:32.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.808][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.812][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-09 16:03:32.813][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-09 16:03:32.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.815][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.818][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-09 16:03:32.819][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-09 16:03:32.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.821][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-09 16:03:32.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.831][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.832][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-09 16:03:32.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.834][ef$get] fields variable is a list.
biodb.TRACE[2025-08-09 16:03:32.838][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-09 16:03:32.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-09 16:03:32.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-09 16:03:32.841][ef$get] fields variable is a list.
biodb.INFO [2025-08-09 16:03:32.847][biodb::testThat]
biodb.INFO [2025-08-09 16:03:32.848][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-09 16:03:32.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:32.849][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:32.851][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-08-09 16:03:32.854][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-08-09 16:03:32.857][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-09 16:03:32.888][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-09 16:03:32.890][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-09 16:03:32.891][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-09 16:03:32.928][biodb::testThat]
biodb.INFO [2025-08-09 16:03:32.929][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-09 16:03:32.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:32.930][biodb::testThat]
biodb.INFO [2025-08-09 16:03:32.935][biodb::testThat]
biodb.INFO [2025-08-09 16:03:32.936][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-09 16:03:32.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:32.938][biodb::testThat]
biodb.WARN [2025-08-09 16:03:32.956][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-09 16:03:32.973][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-09 16:03:32.981][biodb::testThat]
biodb.INFO [2025-08-09 16:03:32.981][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-09 16:03:32.982][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:32.983][biodb::testThat]
biodb.DEBUG[2025-08-09 16:03:33.004][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-08-09 16:03:33.048][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-09 16:03:33.050][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-09 16:03:33.051][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-09 16:03:33.052][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-09 16:03:33.064][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-09 16:03:33.086][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.087][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-09 16:03:33.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:33.089][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.099][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.100][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-09 16:03:33.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:33.101][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.107][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.108][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:33.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:33.110][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.115][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.116][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-09 16:03:33.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-09 16:03:33.118][biodb::testThat]
biodb.INFO [2025-08-09 16:03:33.123][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:33.124][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-09 16:03:33.125][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:33.126][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.127][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.129][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-09 16:03:33.138][biodb::testContext]
biodb.INFO [2025-08-09 16:03:33.139][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:33.140][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-08-09 16:03:33.141][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-09 16:03:33.142][biodb::testContext]
biodb.INFO [2025-08-09 16:03:33.144][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:33.145][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:33.149][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:33.150][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-09 16:03:33.151][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.154][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-09 16:03:33.155][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.159][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-09 16:03:33.160][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.163][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-09 16:03:33.164][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-09 16:03:33.165][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-09 16:03:33.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.168][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-09 16:03:33.169][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-09 16:03:33.170][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.174][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-09 16:03:33.174][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-09 16:03:33.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.178][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-09 16:03:33.179][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-09 16:03:33.180][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-09 16:03:33.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.183][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-09 16:03:33.184][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.187][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-09 16:03:33.188][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-09 16:03:33.189][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-09 16:03:33.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.193][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:33.194][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-09 16:03:33.195][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-09 16:03:33.196][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-09 16:03:33.197][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-09 16:03:33.198][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-09 16:03:33.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.201][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-09 16:03:33.202][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-09 16:03:33.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.205][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-09 16:03:33.206][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-09 16:03:33.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-09 16:03:33.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-09 16:03:33.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.214][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-09 16:03:33.215][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-09 16:03:33.220][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-09 16:03:33.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.223][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-09 16:03:33.224][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-09 16:03:33.227][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-09 16:03:33.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.231][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-09 16:03:33.232][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-09 16:03:33.233][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-09 16:03:33.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.236][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-09 16:03:33.238][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.239][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-09 16:03:33.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:33.242][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.244][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.246][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:33.246][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:33.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.248][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-09 16:03:33.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:33.250][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.251][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.252][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:33.252][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:33.252][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:33.252][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:33.252][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:33.253][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:33.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.256][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:33.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.258][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.259][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.260][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:33.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:33.262][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.263][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.264][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-09 16:03:33.266][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.267][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:33.268][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:33.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.271][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.272][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.273][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:33.274][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:33.275][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.276][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-09 16:03:33.277][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:33.278][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.280][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-09 16:03:33.280][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-09 16:03:33.280][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-09 16:03:33.280][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-09 16:03:33.280][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-09 16:03:33.281][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:33.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.283][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:33.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.286][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.287][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.288][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:33.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:33.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.290][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.291][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-09 16:03:33.293][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.294][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-09 16:03:33.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:33.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.300][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-09 16:03:33.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:33.302][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.303][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-09 16:03:33.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:33.305][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.306][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.307][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:33.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.311][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:33.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.314][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:33.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:33.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.318][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.319][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-09 16:03:33.320][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.321][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-09 16:03:33.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.323][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:33.324][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.325][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.326][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.328][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-09 16:03:33.329][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:33.330][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.331][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-09 16:03:33.332][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:33.333][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.333][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.334][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-09 16:03:33.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.338][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:33.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.345][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:33.347][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:33.348][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.349][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.350][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:33.351][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.398][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[2025-08-09 16:03:33.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.420][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-09 16:03:33.421][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-09 16:03:33.423][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-09 16:03:33.424][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-09 16:03:33.425][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-09 16:03:33.427][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-09 16:03:33.428][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:33.429][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:33.430][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-09 16:03:33.432][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-09 16:03:33.433][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-09 16:03:33.434][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-09 16:03:33.436][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-09 16:03:33.437][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-09 16:03:33.438][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-09 16:03:33.440][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-09 16:03:33.441][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-09 16:03:33.442][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-09 16:03:33.443][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-09 16:03:33.445][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-09 16:03:33.446][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-09 16:03:33.447][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-09 16:03:33.449][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-09 16:03:33.450][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-09 16:03:33.451][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-09 16:03:33.453][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-09 16:03:33.454][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-09 16:03:33.455][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-09 16:03:33.457][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-09 16:03:33.458][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-09 16:03:33.459][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-09 16:03:33.464][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-09 16:03:33.466][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-09 16:03:33.467][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-09 16:03:33.468][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-09 16:03:33.469][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-09 16:03:33.471][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-09 16:03:33.472][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-09 16:03:33.473][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-09 16:03:33.475][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-09 16:03:33.476][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-09 16:03:33.477][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-09 16:03:33.479][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-09 16:03:33.480][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-09 16:03:33.481][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-09 16:03:33.482][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-09 16:03:33.484][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-09 16:03:33.485][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-09 16:03:33.486][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-09 16:03:33.488][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-09 16:03:33.489][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-09 16:03:33.490][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-09 16:03:33.492][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-09 16:03:33.493][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-09 16:03:33.494][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-09 16:03:33.495][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-09 16:03:33.497][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-09 16:03:33.498][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-09 16:03:33.499][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-09 16:03:33.501][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-09 16:03:33.502][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-09 16:03:33.503][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-09 16:03:33.505][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-09 16:03:33.506][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-09 16:03:33.507][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-09 16:03:33.509][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-09 16:03:33.510][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-09 16:03:33.511][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-09 16:03:33.512][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-09 16:03:33.514][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-09 16:03:33.515][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-09 16:03:33.516][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-09 16:03:33.518][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-09 16:03:33.519][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-09 16:03:33.520][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-09 16:03:33.521][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-09 16:03:33.523][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-09 16:03:33.524][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-09 16:03:33.525][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-09 16:03:33.527][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-09 16:03:33.528][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-09 16:03:33.529][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-09 16:03:33.531][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-09 16:03:33.532][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-09 16:03:33.533][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-09 16:03:33.534][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-09 16:03:33.535][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.537][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.549][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[2025-08-09 16:03:33.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-09 16:03:33.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-09 16:03:33.638][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-09 16:03:33.639][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-09 16:03:33.641][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.642][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-09 16:03:33.643][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.644][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-09 16:03:33.645][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.646][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-09 16:03:33.646][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.647][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.648][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-09 16:03:33.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-09 16:03:33.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.651][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-09 16:03:33.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-09 16:03:33.653][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-09 16:03:33.654][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-09 16:03:33.655][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.656][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-09 16:03:33.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-09 16:03:33.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-09 16:03:33.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-09 16:03:33.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-09 16:03:33.662][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:33.662][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-09 16:03:33.662][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-09 16:03:33.662][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-09 16:03:33.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-09 16:03:33.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-09 16:03:33.665][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-09 16:03:33.666][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-09 16:03:33.667][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-09 16:03:33.670][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-09 16:03:33.673][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-09 16:03:33.674][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-09 16:03:33.675][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-09 16:03:33.676][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-09 16:03:33.677][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-09 16:03:33.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-09 16:03:33.679][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-09 16:03:33.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-09 16:03:33.680][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-09 16:03:33.681][FUN] Functions in observer 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 0 | PASS 85 ]

══ 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 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)