Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-20 23:55 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-20 09:55 -0400 (Sat, 20 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-09-20 16:02:34 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 16:03:33 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 59.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-09-20 16:03:29.253][biodb::testContext]
biodb.INFO [2025-09-20 16:03:29.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:29.256][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-20 16:03:29.257][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:29.258][biodb::testContext]
biodb.INFO [2025-09-20 16:03:29.264][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:03:29.265][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:29.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:29.273][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-20 16:03:29.274][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.277][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-20 16:03:29.294][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.297][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-20 16:03:29.298][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.302][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-20 16:03:29.303][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-20 16:03:29.304][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-20 16:03:29.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.307][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-20 16:03:29.308][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-20 16:03:29.309][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.312][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-20 16:03:29.313][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-20 16:03:29.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.316][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[2025-09-20 16:03:29.317][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-20 16:03:29.317][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-20 16:03:29.318][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-20 16:03:29.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.322][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-20 16:03:29.323][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.326][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-20 16:03:29.327][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-20 16:03:29.328][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-20 16:03:29.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.331][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:29.332][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-20 16:03:29.333][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-20 16:03:29.334][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-20 16:03:29.335][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-20 16:03:29.336][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-20 16:03:29.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.339][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-20 16:03:29.340][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-20 16:03:29.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.344][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-20 16:03:29.345][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-20 16:03:29.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.348][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-20 16:03:29.349][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-20 16:03:29.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.352][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-20 16:03:29.353][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-20 16:03:29.354][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-20 16:03:29.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.357][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:29.358][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-20 16:03:29.362][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-20 16:03:29.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.365][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-20 16:03:29.366][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-20 16:03:29.367][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-20 16:03:29.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.378][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-20 16:03:29.408][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.423][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-20 16:03:29.424][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:29.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.428][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.429][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:29.430][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:29.431][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.432][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-20 16:03:29.433][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:29.434][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.435][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.436][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:29.436][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:29.436][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:29.436][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:29.436][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:29.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:29.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:29.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.443][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:29.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:29.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.447][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.448][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-20 16:03:29.449][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.450][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:29.451][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:29.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.455][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.456][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.457][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:29.458][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:29.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.460][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-20 16:03:29.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:29.461][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.462][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:29.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:29.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:29.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:29.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:29.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:29.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:29.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.469][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.470][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.471][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:29.472][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:29.473][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.474][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.475][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-20 16:03:29.477][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.478][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-20 16:03:29.479][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:29.480][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.481][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.482][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.483][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.484][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:29.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:29.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.487][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-20 16:03:29.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:29.489][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.491][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.492][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:29.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.494][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:29.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.497][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.498][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.499][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:29.499][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:29.500][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.501][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.502][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-20 16:03:29.504][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.505][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:29.506][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.507][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:29.508][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.509][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.511][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.511][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:29.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:29.513][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.514][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-20 16:03:29.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:29.516][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.517][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.518][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.519][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:29.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.522][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:29.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.523][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.524][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.525][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:29.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:29.528][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.529][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:29.538][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.551][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[2025-09-20 16:03:29.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.559][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[2025-09-20 16:03:29.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.564][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[2025-09-20 16:03:29.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.568][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[2025-09-20 16:03:29.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.572][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[2025-09-20 16:03:29.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.576][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[2025-09-20 16:03:29.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.580][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[2025-09-20 16:03:29.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.597][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[2025-09-20 16:03:29.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.605][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[2025-09-20 16:03:29.606][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-20 16:03:29.610][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-20 16:03:29.611][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-20 16:03:29.613][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-20 16:03:29.614][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-20 16:03:29.615][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:03:29.617][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:29.618][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:29.619][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-20 16:03:29.621][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:03:29.622][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:03:29.623][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-20 16:03:29.624][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:29.626][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:29.627][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-20 16:03:29.628][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:03:29.630][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-20 16:03:29.631][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-20 16:03:29.632][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-20 16:03:29.634][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-20 16:03:29.635][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-20 16:03:29.636][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-20 16:03:29.637][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-20 16:03:29.639][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-20 16:03:29.640][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-20 16:03:29.641][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-20 16:03:29.643][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-20 16:03:29.644][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-20 16:03:29.645][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-20 16:03:29.646][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-20 16:03:29.648][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-20 16:03:29.649][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-20 16:03:29.650][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-20 16:03:29.652][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-20 16:03:29.653][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-20 16:03:29.654][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-20 16:03:29.655][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-20 16:03:29.657][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-20 16:03:29.658][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-20 16:03:29.659][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-20 16:03:29.661][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-20 16:03:29.662][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-20 16:03:29.663][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-20 16:03:29.665][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-20 16:03:29.666][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-20 16:03:29.667][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-20 16:03:29.668][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-20 16:03:29.670][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-20 16:03:29.671][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-20 16:03:29.672][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-20 16:03:29.674][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-20 16:03:29.675][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-20 16:03:29.676][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-20 16:03:29.677][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-20 16:03:29.679][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-20 16:03:29.680][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-20 16:03:29.681][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-20 16:03:29.683][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-20 16:03:29.684][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-20 16:03:29.685][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-20 16:03:29.687][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-20 16:03:29.688][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-20 16:03:29.689][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-20 16:03:29.690][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-20 16:03:29.692][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-20 16:03:29.693][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-20 16:03:29.694][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-20 16:03:29.696][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-20 16:03:29.701][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-20 16:03:29.702][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-20 16:03:29.703][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-20 16:03:29.705][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-20 16:03:29.706][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-20 16:03:29.707][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-20 16:03:29.708][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-20 16:03:29.710][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-20 16:03:29.711][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-20 16:03:29.712][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-20 16:03:29.714][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-20 16:03:29.715][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-20 16:03:29.716][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-20 16:03:29.717][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-20 16:03:29.719][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-20 16:03:29.724][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-20 16:03:29.726][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:03:29.729][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:29.729][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.731][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.732][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[2025-09-20 16:03:29.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:29.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:29.829][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:29.838][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-20 16:03:29.840][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.841][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-20 16:03:29.842][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.843][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:29.844][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.845][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-20 16:03:29.846][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.848][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-20 16:03:29.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:29.850][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.851][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-20 16:03:29.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-20 16:03:29.852][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-20 16:03:29.853][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:29.858][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.859][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-20 16:03:29.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:29.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:29.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:29.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:29.871][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-20 16:03:29.871][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-20 16:03:29.871][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-20 16:03:29.871][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-20 16:03:29.872][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:29.873][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:29.874][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:29.875][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:29.883][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-20 16:03:29.911][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-20 16:03:29.927][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-20 16:03:29.937][biodb::testThat]
biodb.INFO [2025-09-20 16:03:29.938][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-20 16:03:29.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:29.940][biodb::testThat]
biodb.TRACE[2025-09-20 16:03:29.943][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-09-20 16:03:29.945][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-20 16:03:29.948][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-20 16:03:29.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-20 16:03:29.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:29.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:29.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:29.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:29.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:29.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-20 16:03:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:29.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:29.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:29.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:29.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.096][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:30.152][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-09-20 16:03:30.154][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.161][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.165][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:30.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:30.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.185][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.219][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.246][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.249][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.271][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.273][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.295][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.298][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.323][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.324][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.326][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.351][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.361][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.362][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.364][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.368][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.371][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.374][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.375][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.377][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.381][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.384][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.387][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.390][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.407][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-09-20 16:03:30.498][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-20 16:03:30.500][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-20 16:03:30.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-20 16:03:30.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:30.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:30.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:30.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:30.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:30.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-20 16:03:30.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.546][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.559][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.618][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.622][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:03:30.663][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-09-20 16:03:30.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:03:30.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:30.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:03:30.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:30.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:03:30.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.708][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.741][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.745][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.749][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-20 16:03:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.786][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.787][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.789][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.801][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.805][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.809][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.813][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.814][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.816][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.837][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.841][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.842][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.844][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:30.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:30.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.867][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.868][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.870][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.871][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.893][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.894][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.896][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.924][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.926][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.949][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.952][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.963][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:03:30.964][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:03:30.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.966][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.969][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.970][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:03:30.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.972][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.976][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:03:30.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:03:30.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.979][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.983][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:03:30.984][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:03:30.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.985][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.989][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.990][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:03:30.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.992][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:30.996][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.997][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-20 16:03:30.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:30.999][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:03:31.003][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:03:31.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:03:31.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:03:31.005][ef$get] fields variable is a list.
biodb.INFO [2025-09-20 16:03:31.012][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.013][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-20 16:03:31.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.014][biodb::testThat]
biodb.DEBUG[2025-09-20 16:03:31.016][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-09-20 16:03:31.018][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-09-20 16:03:31.021][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:31.053][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-20 16:03:31.054][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-20 16:03:31.055][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-20 16:03:31.093][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.094][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-20 16:03:31.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.096][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.101][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.102][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-20 16:03:31.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.104][biodb::testThat]
biodb.WARN [2025-09-20 16:03:31.122][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-20 16:03:31.140][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-20 16:03:31.147][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.148][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-20 16:03:31.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.150][biodb::testThat]
biodb.DEBUG[2025-09-20 16:03:31.170][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-09-20 16:03:31.215][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:03:31.216][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-20 16:03:31.217][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-20 16:03:31.219][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-20 16:03:31.231][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-20 16:03:31.253][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.254][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-20 16:03:31.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.256][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.266][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.267][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-20 16:03:31.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.269][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.275][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.276][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-20 16:03:31.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.278][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.283][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.284][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-20 16:03:31.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:03:31.286][biodb::testThat]
biodb.INFO [2025-09-20 16:03:31.291][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-20 16:03:31.292][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-20 16:03:31.293][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-20 16:03:31.293][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.295][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.297][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-20 16:03:31.306][biodb::testContext]
biodb.INFO [2025-09-20 16:03:31.307][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:31.308][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-09-20 16:03:31.309][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:03:31.310][biodb::testContext]
biodb.INFO [2025-09-20 16:03:31.312][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:03:31.314][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:31.317][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:31.318][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-20 16:03:31.319][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.322][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-20 16:03:31.323][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.327][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-20 16:03:31.328][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.331][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-20 16:03:31.332][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-20 16:03:31.333][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-20 16:03:31.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.337][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-20 16:03:31.338][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-20 16:03:31.339][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.342][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-20 16:03:31.343][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-20 16:03:31.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.346][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-20 16:03:31.347][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-20 16:03:31.348][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-20 16:03:31.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.352][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-20 16:03:31.353][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.356][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-20 16:03:31.357][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-20 16:03:31.358][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-20 16:03:31.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.362][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:31.363][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-20 16:03:31.364][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-20 16:03:31.365][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-20 16:03:31.366][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-20 16:03:31.367][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-20 16:03:31.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.370][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-20 16:03:31.371][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-20 16:03:31.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.375][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-20 16:03:31.376][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-20 16:03:31.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.379][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-20 16:03:31.380][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-20 16:03:31.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.384][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-20 16:03:31.385][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-20 16:03:31.386][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-20 16:03:31.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.393][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:03:31.394][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-20 16:03:31.398][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-20 16:03:31.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.401][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-20 16:03:31.402][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-20 16:03:31.403][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-20 16:03:31.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.407][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-20 16:03:31.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.410][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-20 16:03:31.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.411][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:31.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.413][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.414][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.415][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.416][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:31.417][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:31.418][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.419][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-20 16:03:31.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:31.421][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.422][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.423][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:31.423][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:31.423][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:31.423][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:31.423][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:31.424][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:31.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.427][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:31.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.430][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:31.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:31.433][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.434][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.435][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-20 16:03:31.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:31.439][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.440][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:31.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.441][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.442][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.443][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.444][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:31.445][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:31.446][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.447][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-20 16:03:31.448][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:31.449][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.450][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.451][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:03:31.451][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:03:31.451][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:03:31.451][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:03:31.451][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:03:31.452][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:31.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.455][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:31.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.457][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.458][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.459][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:31.460][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:31.461][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.462][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.463][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-20 16:03:31.465][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.466][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-20 16:03:31.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.467][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:31.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.470][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.472][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:03:31.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:31.474][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.475][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-20 16:03:31.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:31.477][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.478][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.479][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.480][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:31.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:31.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.486][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:31.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:31.489][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.490][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.491][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-20 16:03:31.493][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.493][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:03:31.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:31.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.500][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:03:31.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:31.502][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.503][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-20 16:03:31.504][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:31.505][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.506][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.507][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.508][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:03:31.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:31.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.518][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:31.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:31.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.521][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.523][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:31.524][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.537][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[2025-09-20 16:03:31.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.546][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[2025-09-20 16:03:31.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.559][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[2025-09-20 16:03:31.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.576][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[2025-09-20 16:03:31.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.580][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[2025-09-20 16:03:31.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.588][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[2025-09-20 16:03:31.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.594][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-20 16:03:31.595][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-20 16:03:31.596][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-20 16:03:31.598][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-20 16:03:31.599][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-20 16:03:31.600][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:03:31.602][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:31.603][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:31.604][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-20 16:03:31.606][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:03:31.607][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:03:31.608][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-20 16:03:31.610][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-20 16:03:31.611][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-20 16:03:31.612][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-20 16:03:31.614][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:03:31.615][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-20 16:03:31.616][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-20 16:03:31.618][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-20 16:03:31.619][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-20 16:03:31.620][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-20 16:03:31.622][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-20 16:03:31.623][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-20 16:03:31.624][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-20 16:03:31.626][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-20 16:03:31.627][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-20 16:03:31.628][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-20 16:03:31.630][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-20 16:03:31.631][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-20 16:03:31.632][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-20 16:03:31.634][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-20 16:03:31.635][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-20 16:03:31.640][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-20 16:03:31.641][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-20 16:03:31.643][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-20 16:03:31.644][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-20 16:03:31.645][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-20 16:03:31.646][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-20 16:03:31.648][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-20 16:03:31.649][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-20 16:03:31.650][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-20 16:03:31.652][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-20 16:03:31.653][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-20 16:03:31.654][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-20 16:03:31.656][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-20 16:03:31.657][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-20 16:03:31.658][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-20 16:03:31.660][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-20 16:03:31.661][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-20 16:03:31.663][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-20 16:03:31.664][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-20 16:03:31.665][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-20 16:03:31.666][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-20 16:03:31.668][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-20 16:03:31.669][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-20 16:03:31.670][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-20 16:03:31.672][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-20 16:03:31.673][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-20 16:03:31.674][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-20 16:03:31.676][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-20 16:03:31.677][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-20 16:03:31.678][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-20 16:03:31.680][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-20 16:03:31.681][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-20 16:03:31.682][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-20 16:03:31.684][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-20 16:03:31.685][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-20 16:03:31.686][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-20 16:03:31.688][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-20 16:03:31.689][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-20 16:03:31.690][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-20 16:03:31.692][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-20 16:03:31.693][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-20 16:03:31.694][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-20 16:03:31.696][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-20 16:03:31.697][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-20 16:03:31.698][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-20 16:03:31.700][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-20 16:03:31.701][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-20 16:03:31.702][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-20 16:03:31.704][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-20 16:03:31.705][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-20 16:03:31.706][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-20 16:03:31.708][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-20 16:03:31.709][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:03:31.710][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:03:31.711][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.713][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.749][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[2025-09-20 16:03:31.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.755][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[2025-09-20 16:03:31.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:03:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:03:31.814][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-20 16:03:31.815][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-20 16:03:31.817][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.818][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-20 16:03:31.819][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:03:31.821][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.822][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-20 16:03:31.823][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.824][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.825][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-20 16:03:31.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:03:31.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.828][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-20 16:03:31.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-20 16:03:31.830][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-20 16:03:31.831][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-20 16:03:31.832][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.833][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-20 16:03:31.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:03:31.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:03:31.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:03:31.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:03:31.839][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-20 16:03:31.839][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-20 16:03:31.839][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-20 16:03:31.839][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-20 16:03:31.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:03:31.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:03:31.842][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-20 16:03:31.842][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:03:31.844][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-20 16:03:31.847][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-20 16:03:31.850][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-20 16:03:31.851][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-20 16:03:31.852][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-20 16:03:31.853][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-20 16:03:31.854][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:03:31.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:03:31.855][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:03:31.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:03:31.857][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:03:31.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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