Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-28 23:55 -0400 (Sat, 28 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4687
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-28 09:55 -0400 (Sat, 28 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-03-28 16:02:17 -0400 (Sat, 28 Mar 2026)
EndedAt: 2026-03-28 16:03:21 -0400 (Sat, 28 Mar 2026)
EllapsedTime: 64.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-03-28 16:03:17.199][biodb::testContext]
biodb.INFO [2026-03-28 16:03:17.200][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:03:17.201][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-28 16:03:17.202][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:03:17.203][biodb::testContext]
biodb.INFO [2026-03-28 16:03:17.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:03:17.211][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:03:17.217][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:17.218][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:03:17.219][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.222][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:03:17.239][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.243][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:03:17.244][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.247][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:03:17.248][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:03:17.249][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:03:17.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.253][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:03:17.254][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:03:17.255][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.258][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:03:17.259][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:03:17.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.262][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:03:17.263][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:03:17.264][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:03:17.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.268][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:03:17.268][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.272][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:03:17.273][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:03:17.274][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:03:17.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.277][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:03:17.278][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:03:17.279][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:03:17.280][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:03:17.281][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:03:17.282][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:03:17.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.285][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:03:17.286][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:03:17.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.290][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:03:17.291][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:03:17.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.294][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:03:17.295][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:03:17.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.298][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:03:17.299][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:03:17.300][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:03:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.304][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:03:17.305][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:03:17.308][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:03:17.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.312][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:03:17.313][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:03:17.314][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:03:17.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.320][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:03:17.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.371][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:03:17.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:17.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.378][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:03:17.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:17.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.380][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:03:17.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:17.382][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:03:17.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:03:17.384][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:03:17.384][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:03:17.384][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:03:17.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:17.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:17.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.391][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:17.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:17.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.395][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.396][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:03:17.398][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.399][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:03:17.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:17.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.405][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:03:17.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:17.407][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.408][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:03:17.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:17.410][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.412][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:03:17.412][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:03:17.412][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:03:17.412][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:03:17.412][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:03:17.413][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:17.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.415][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:17.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.418][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.419][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:17.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:17.421][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.422][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.423][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:03:17.425][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.426][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:03:17.427][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.428][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:17.429][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.431][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.432][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.433][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:03:17.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:17.434][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.435][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:03:17.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:17.437][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.439][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:17.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.443][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:17.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.445][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.446][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:17.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:17.449][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.450][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.451][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:03:17.452][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.453][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:03:17.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:17.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.458][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.460][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:03:17.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:17.462][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.463][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:03:17.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:17.465][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.465][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.466][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.467][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:17.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:17.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.474][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:17.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:17.476][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.477][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.481][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:17.482][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.482][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[2026-03-28 16:03:17.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.566][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:03:17.573][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:03:17.574][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:03:17.576][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:03:17.577][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:03:17.579][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:03:17.580][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:03:17.582][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:03:17.583][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:03:17.584][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:03:17.586][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:03:17.604][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:03:17.606][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:03:17.607][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:03:17.609][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:03:17.610][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:03:17.611][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:03:17.613][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:03:17.614][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:03:17.616][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:03:17.617][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:03:17.619][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:03:17.620][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:03:17.622][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:03:17.623][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:03:17.625][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:03:17.626][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:03:17.628][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:03:17.629][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:03:17.630][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:03:17.632][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:03:17.633][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:03:17.635][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:03:17.637][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:03:17.638][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:03:17.639][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:03:17.641][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:03:17.642][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:03:17.644][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:03:17.645][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:03:17.646][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:03:17.648][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:03:17.649][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:03:17.651][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:03:17.652][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:03:17.654][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:03:17.655][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:03:17.656][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:03:17.658][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:03:17.659][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:03:17.661][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:03:17.662][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:03:17.664][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:03:17.665][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:03:17.666][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:03:17.668][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:03:17.669][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:03:17.671][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:03:17.672][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:03:17.674][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:03:17.675][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:03:17.676][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:03:17.678][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:03:17.679][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:03:17.681][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:03:17.682][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:03:17.683][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:03:17.685][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:03:17.686][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:03:17.688][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:03:17.689][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:03:17.691][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:03:17.692][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:03:17.693][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:03:17.695][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:03:17.696][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:03:17.698][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:03:17.699][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:03:17.700][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:03:17.702][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:03:17.703][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:03:17.705][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:03:17.706][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:03:17.713][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:03:17.714][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:03:17.718][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:17.719][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.720][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:17.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:17.827][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-28 16:03:17.835][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-28 16:03:17.837][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.838][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-28 16:03:17.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.840][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:17.841][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.842][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-28 16:03:17.843][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.845][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-28 16:03:17.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:17.847][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.848][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-28 16:03:17.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-28 16:03:17.850][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-28 16:03:17.851][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:17.851][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.852][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:03:17.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.855][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:17.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:17.857][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:17.858][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:17.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:03:17.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:03:17.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-28 16:03:17.859][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-28 16:03:17.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:17.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:17.861][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:17.862][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:17.868][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-28 16:03:17.889][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-28 16:03:17.903][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-28 16:03:17.911][biodb::testThat]
biodb.INFO [2026-03-28 16:03:17.912][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:03:17.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:17.914][biodb::testThat]
biodb.TRACE[2026-03-28 16:03:17.917][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-03-28 16:03:17.919][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:03:17.922][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-28 16:03:17.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:03:17.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:17.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:17.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:17.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:17.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:17.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:03:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:17.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:17.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:17.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:17.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:17.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:17.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:17.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.051][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.059][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:03:18.115][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-03-28 16:03:18.118][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.121][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:03:18.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:03:18.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.129][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:03:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:03:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.149][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.187][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.191][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.211][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.213][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.214][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.237][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.238][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.239][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.240][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.263][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.264][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.265][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.265][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.280][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.288][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.289][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.290][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.291][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.313][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.314][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.315][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.316][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.327][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.329][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.330][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.334][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.335][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.336][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.337][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.346][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.346][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.347][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.351][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.352][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.354][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.358][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.359][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.360][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.361][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.376][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-03-28 16:03:18.410][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:03:18.411][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-28 16:03:18.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:03:18.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:18.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:18.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:18.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:18.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:18.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:03:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.566][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:03:18.604][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-03-28 16:03:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:03:18.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:03:18.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:03:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:03:18.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:03:18.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.647][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.678][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.686][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:03:18.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.719][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.721][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.722][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.734][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.738][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.745][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.746][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.747][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.748][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.749][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.771][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.773][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.774][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.796][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.797][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.798][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.799][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.822][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.824][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.825][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.847][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.848][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.849][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.850][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.877][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.878][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.879][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.879][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.891][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:03:18.892][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:03:18.893][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.894][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.898][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.899][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:03:18.900][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.901][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.904][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:03:18.905][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:03:18.906][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.907][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.911][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:03:18.912][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:03:18.913][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.914][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.918][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.919][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:03:18.920][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.921][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.924][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.925][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:03:18.926][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.927][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:03:18.931][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:03:18.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:03:18.933][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:03:18.934][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:03:18.940][biodb::testThat]
biodb.INFO [2026-03-28 16:03:18.941][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:03:18.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:18.943][biodb::testThat]
biodb.DEBUG[2026-03-28 16:03:18.945][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-03-28 16:03:18.948][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-03-28 16:03:18.951][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-28 16:03:18.978][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-28 16:03:18.980][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-28 16:03:18.981][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-28 16:03:19.110][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.111][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:03:19.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.112][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.118][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.119][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:03:19.120][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.121][biodb::testThat]
biodb.WARN [2026-03-28 16:03:19.136][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-28 16:03:19.158][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-28 16:03:19.165][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.166][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:03:19.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.167][biodb::testThat]
biodb.DEBUG[2026-03-28 16:03:19.183][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-03-28 16:03:19.227][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:03:19.229][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-28 16:03:19.230][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-28 16:03:19.231][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-28 16:03:19.243][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-28 16:03:19.297][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.298][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:03:19.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.300][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.307][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.308][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:03:19.309][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.309][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.316][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.317][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:03:19.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.319][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.324][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.325][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:03:19.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:03:19.327][biodb::testThat]
biodb.INFO [2026-03-28 16:03:19.332][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:03:19.333][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-28 16:03:19.334][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:03:19.335][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.336][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.338][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-28 16:03:19.348][biodb::testContext]
biodb.INFO [2026-03-28 16:03:19.349][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:03:19.350][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-03-28 16:03:19.350][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:03:19.351][biodb::testContext]
biodb.INFO [2026-03-28 16:03:19.353][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:03:19.355][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:03:19.358][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:19.359][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:03:19.360][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.364][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:03:19.365][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.368][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:03:19.369][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.372][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:03:19.373][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:03:19.374][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:03:19.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.378][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:03:19.379][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:03:19.380][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.383][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:03:19.384][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:03:19.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.387][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:03:19.388][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:03:19.389][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:03:19.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.393][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:03:19.394][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.397][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:03:19.398][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:03:19.399][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:03:19.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.402][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:03:19.403][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:03:19.404][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:03:19.405][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:03:19.406][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:03:19.407][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:03:19.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.411][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:03:19.412][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:03:19.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.415][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:03:19.416][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:03:19.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.419][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:03:19.420][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:03:19.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.424][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:03:19.425][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:03:19.426][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:03:19.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.429][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:03:19.434][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:03:19.438][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:03:19.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.440][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[2026-03-28 16:03:19.441][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:03:19.442][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:03:19.443][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:03:19.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.447][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:03:19.448][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.449][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:03:19.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:19.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:03:19.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:19.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.459][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:03:19.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:19.461][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.462][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:03:19.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:03:19.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:03:19.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:03:19.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:03:19.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:19.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:19.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.469][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.470][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.471][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:19.472][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:19.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.473][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.475][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:03:19.476][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.477][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:03:19.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:19.480][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.481][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.482][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.483][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.484][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:03:19.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:19.486][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.487][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:03:19.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:19.488][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.490][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:03:19.490][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:03:19.490][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:03:19.490][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:03:19.490][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:03:19.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:19.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:19.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.497][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.497][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.498][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:19.499][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:19.500][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.501][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.502][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:03:19.504][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.505][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:03:19.506][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.507][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:19.508][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.509][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:03:19.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:19.513][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.514][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:03:19.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:19.516][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.517][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.518][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.519][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:19.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.522][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:19.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.525][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:19.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:19.528][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.529][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.530][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:03:19.532][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.533][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:03:19.533][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.534][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:19.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.537][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.539][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:03:19.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:19.541][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.542][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:03:19.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:19.544][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.545][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.546][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.547][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:03:19.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:19.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.553][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.554][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:19.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:19.555][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.556][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.558][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:19.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.601][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[2026-03-28 16:03:19.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.613][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[2026-03-28 16:03:19.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.631][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:03:19.632][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:03:19.634][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:03:19.635][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:03:19.636][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:03:19.638][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:03:19.639][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:03:19.640][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:03:19.642][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:03:19.643][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:03:19.644][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:03:19.646][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:03:19.647][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:03:19.648][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:03:19.650][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:03:19.651][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:03:19.652][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:03:19.654][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:03:19.655][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:03:19.656][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:03:19.657][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:03:19.659][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:03:19.660][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:03:19.661][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:03:19.663][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:03:19.664][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:03:19.665][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:03:19.667][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:03:19.668][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:03:19.669][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:03:19.671][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:03:19.672][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:03:19.673][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:03:19.674][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:03:19.676][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:03:19.677][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:03:19.678][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:03:19.680][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:03:19.681][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:03:19.682][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:03:19.684][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:03:19.685][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:03:19.686][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:03:19.688][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:03:19.689][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:03:19.690][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:03:19.691][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:03:19.693][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:03:19.694][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:03:19.695][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:03:19.697][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:03:19.698][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:03:19.699][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:03:19.701][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:03:19.702][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:03:19.703][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:03:19.705][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:03:19.706][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:03:19.707][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:03:19.708][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:03:19.710][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:03:19.711][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:03:19.712][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:03:19.714][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:03:19.715][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:03:19.716][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:03:19.718][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:03:19.719][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:03:19.720][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:03:19.721][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:03:19.723][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:03:19.724][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:03:19.725][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:03:19.727][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:03:19.728][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:03:19.729][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:03:19.731][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:03:19.736][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:03:19.737][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:03:19.739][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:03:19.740][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:03:19.741][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:03:19.742][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:03:19.744][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:03:19.745][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:03:19.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:03:19.747][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.749][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:03:19.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:03:19.845][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-28 16:03:19.846][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-28 16:03:19.848][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.849][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-28 16:03:19.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:03:19.852][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.853][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-28 16:03:19.854][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.854][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.855][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-28 16:03:19.856][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:03:19.857][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.858][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-28 16:03:19.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-28 16:03:19.860][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-28 16:03:19.861][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:03:19.862][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.863][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:03:19.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.866][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:03:19.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:03:19.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:03:19.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:03:19.869][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:03:19.869][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:03:19.869][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-28 16:03:19.869][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-28 16:03:19.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:03:19.871][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:03:19.872][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:03:19.873][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:03:19.874][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-28 16:03:19.877][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-28 16:03:19.884][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-28 16:03:19.885][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:03:19.886][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-28 16:03:19.887][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:03:19.888][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:03:19.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:03:19.890][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:03:19.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:03:19.891][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:03:19.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

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

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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)