Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-01 23:55 -0400 (Sat, 01 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-01 09:55 -0400 (Sat, 01 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2025-11-01 16:01:14 -0400 (Sat, 01 Nov 2025)
EndedAt: 2025-11-01 16:02:12 -0400 (Sat, 01 Nov 2025)
EllapsedTime: 58.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-11-01 16:02:09.269][biodb::testContext]
biodb.INFO [2025-11-01 16:02:09.272][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:09.273][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-01 16:02:09.274][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:09.275][biodb::testContext]
biodb.INFO [2025-11-01 16:02:09.280][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:09.282][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:09.288][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:09.289][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:09.290][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.293][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:09.309][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.313][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:09.314][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.326][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:09.327][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:09.327][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:09.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.330][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[2025-11-01 16:02:09.331][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:09.331][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:09.332][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.336][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:09.336][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:09.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.340][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:09.341][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:09.342][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:09.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:09.346][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.349][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:09.350][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:09.351][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:09.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.354][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:09.355][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:09.356][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:09.357][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:09.357][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:09.358][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:09.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.361][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[2025-11-01 16:02:09.362][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:09.363][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:09.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.366][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:09.367][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:09.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.369][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[2025-11-01 16:02:09.370][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:09.371][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:09.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.374][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:09.375][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:09.376][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:09.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.378][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[2025-11-01 16:02:09.379][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:09.380][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:09.399][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:09.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.403][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:09.404][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:09.405][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:09.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.410][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:09.438][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.451][self$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[2025-11-01 16:02:09.452][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.454][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:09.455][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.456][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.457][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.458][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:09.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:09.460][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.461][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:09.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:09.463][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.465][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:09.465][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:09.465][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:09.465][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:09.465][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:09.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:09.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:09.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.472][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:09.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:09.474][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.475][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.476][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:09.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.479][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:09.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.480][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:09.486][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.489][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:09.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:09.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.492][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:09.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:09.494][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:09.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:09.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:09.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:09.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.501][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.502][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.503][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:09.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:09.505][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.506][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.507][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:09.508][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.509][self$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[2025-11-01 16:02:09.510][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:09.512][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.513][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.514][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.515][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.516][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:09.517][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:09.518][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.518][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:09.519][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:09.520][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.521][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.522][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.523][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:09.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.525][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:09.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.528][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.529][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:09.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:09.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.532][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.533][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:09.535][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.536][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:09.536][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.537][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:09.538][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.539][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.540][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.541][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.542][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:09.543][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:09.544][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.545][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:09.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:09.546][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.547][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.548][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.549][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:09.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.552][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:09.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.554][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.555][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:09.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:09.557][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.558][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.562][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:09.563][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.564][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[2025-11-01 16:02:09.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.568][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[2025-11-01 16:02:09.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.572][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[2025-11-01 16:02:09.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.576][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[2025-11-01 16:02:09.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.580][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[2025-11-01 16:02:09.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.584][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[2025-11-01 16:02:09.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.588][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[2025-11-01 16:02:09.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.629][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:09.638][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:09.639][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:09.640][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:09.641][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:09.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:09.644][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:09.645][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:09.646][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:09.647][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:09.648][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:09.650][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:09.651][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:09.652][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:09.653][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:09.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:09.656][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:09.657][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:09.658][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:09.659][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:09.661][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:09.662][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:09.663][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:09.665][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:09.666][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:09.667][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:09.668][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:09.669][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:09.671][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:09.672][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:09.673][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:09.674][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:09.676][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:09.677][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:09.678][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:09.679][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:09.680][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:09.682][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:09.683][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:09.684][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:09.685][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:09.686][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:09.688][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:09.689][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:09.690][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:09.691][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:09.692][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:09.694][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:09.695][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:09.696][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:09.697][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:09.699][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:09.700][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:09.701][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:09.702][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:09.704][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:09.705][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:09.706][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:09.707][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:09.709][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:09.710][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:09.711][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:09.712][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:09.713][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:09.715][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:09.716][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:09.717][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:09.718][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:09.719][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:09.721][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:09.722][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:09.723][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:09.724][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:09.725][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:09.727][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:09.728][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:09.729][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:09.730][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:09.732][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:09.733][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:09.734][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:09.735][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:09.736][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:09.741][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:09.743][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:09.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:09.747][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.748][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.749][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[2025-11-01 16:02:09.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.789][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[2025-11-01 16:02:09.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.795][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[2025-11-01 16:02:09.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.822][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[2025-11-01 16:02:09.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.828][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[2025-11-01 16:02:09.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:09.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:09.846][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:09.855][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-01 16:02:09.857][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.857][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-01 16:02:09.858][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.859][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:09.860][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.861][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-01 16:02:09.862][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.864][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-01 16:02:09.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:09.865][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.866][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-01 16:02:09.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-01 16:02:09.868][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-01 16:02:09.869][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:09.870][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.871][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:09.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:09.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:09.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:09.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:09.877][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:09.877][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:09.877][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-01 16:02:09.877][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-01 16:02:09.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:09.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:09.879][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:09.880][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:09.885][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-01 16:02:09.906][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-01 16:02:09.920][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-01 16:02:09.935][biodb::testThat]
biodb.INFO [2025-11-01 16:02:09.936][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-01 16:02:09.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:09.938][biodb::testThat]
biodb.TRACE[2025-11-01 16:02:09.941][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-11-01 16:02:09.942][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:09.945][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-01 16:02:09.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:09.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:09.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:09.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:09.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:09.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:09.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:09.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:09.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:09.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:09.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:09.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:09.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:09.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:09.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.001][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.066][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.080][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:10.135][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-11-01 16:02:10.137][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:10.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:10.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.147][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:10.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:10.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.167][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.238][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.242][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.267][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.268][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.270][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.293][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.293][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.295][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.318][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.319][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.321][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.347][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.348][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.349][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.371][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.372][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.374][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.386][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.387][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.389][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.394][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.395][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.397][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.405][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.409][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.410][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.412][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.416][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.419][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.433][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-11-01 16:02:10.468][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-11-01 16:02:10.469][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-11-01 16:02:10.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-01 16:02:10.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:10.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:10.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:10.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:10.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:10.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-01 16:02:10.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.510][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.514][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.578][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.581][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.588][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-01 16:02:10.613][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-11-01 16:02:10.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.634][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-01 16:02:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:10.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-01 16:02:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:10.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-01 16:02:10.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.654][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.689][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.693][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.697][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-11-01 16:02:10.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.729][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.730][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.733][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.751][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.757][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.762][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.764][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.766][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.768][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.797][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.798][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.800][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.825][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.829][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.833][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.836][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.859][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.860][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.862][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.885][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.886][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.887][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.911][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.913][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.926][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-01 16:02:10.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-01 16:02:10.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.928][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.937][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.939][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-01 16:02:10.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.940][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.945][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-01 16:02:10.946][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-01 16:02:10.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.948][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.953][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-01 16:02:10.954][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-01 16:02:10.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.956][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.961][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.962][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-01 16:02:10.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.963][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.968][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.969][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-01 16:02:10.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.971][ef$get] fields variable is a list.
biodb.TRACE[2025-11-01 16:02:10.975][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-01 16:02:10.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-01 16:02:10.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-01 16:02:10.978][ef$get] fields variable is a list.
biodb.INFO [2025-11-01 16:02:10.986][biodb::testThat]
biodb.INFO [2025-11-01 16:02:10.987][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-01 16:02:10.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:10.989][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:10.991][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-11-01 16:02:10.996][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-11-01 16:02:10.998][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:11.023][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-01 16:02:11.024][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-01 16:02:11.025][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-11-01 16:02:11.066][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.067][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-01 16:02:11.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.069][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.076][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.077][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-01 16:02:11.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.078][biodb::testThat]
biodb.WARN [2025-11-01 16:02:11.095][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-11-01 16:02:11.111][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-11-01 16:02:11.121][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.122][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-01 16:02:11.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.123][biodb::testThat]
biodb.DEBUG[2025-11-01 16:02:11.138][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-11-01 16:02:11.182][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-01 16:02:11.184][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-11-01 16:02:11.185][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-11-01 16:02:11.186][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-11-01 16:02:11.197][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-11-01 16:02:11.219][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.220][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-01 16:02:11.220][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.221][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.229][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.230][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-01 16:02:11.230][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.231][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.238][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.239][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:11.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.241][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.247][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.252][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-01 16:02:11.253][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-01 16:02:11.254][biodb::testThat]
biodb.INFO [2025-11-01 16:02:11.261][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:11.262][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-01 16:02:11.262][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:11.263][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.265][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.266][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-11-01 16:02:11.276][biodb::testContext]
biodb.INFO [2025-11-01 16:02:11.277][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:11.278][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-11-01 16:02:11.279][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-01 16:02:11.279][biodb::testContext]
biodb.INFO [2025-11-01 16:02:11.281][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:11.283][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:11.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:11.287][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-01 16:02:11.288][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.291][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-01 16:02:11.292][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.296][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-01 16:02:11.297][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.300][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-01 16:02:11.301][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-01 16:02:11.302][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-01 16:02:11.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.305][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-01 16:02:11.306][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-01 16:02:11.307][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.310][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-01 16:02:11.311][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-01 16:02:11.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.314][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-01 16:02:11.315][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-01 16:02:11.316][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-01 16:02:11.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.319][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-01 16:02:11.320][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.323][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-01 16:02:11.324][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-01 16:02:11.325][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-01 16:02:11.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.328][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:11.329][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-01 16:02:11.330][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-01 16:02:11.331][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-01 16:02:11.332][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-01 16:02:11.333][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-01 16:02:11.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.336][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-01 16:02:11.337][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-01 16:02:11.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.340][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-01 16:02:11.341][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-01 16:02:11.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.344][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-01 16:02:11.345][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-01 16:02:11.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.347][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[2025-11-01 16:02:11.348][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-01 16:02:11.349][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-01 16:02:11.350][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-01 16:02:11.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.353][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-01 16:02:11.354][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-01 16:02:11.376][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-01 16:02:11.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.383][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[2025-11-01 16:02:11.384][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-01 16:02:11.385][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-01 16:02:11.386][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-01 16:02:11.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.389][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-01 16:02:11.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.404][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-01 16:02:11.406][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:11.408][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.408][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.411][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:11.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:11.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.414][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-01 16:02:11.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:11.416][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.416][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.417][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:11.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:11.417][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:11.417][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:11.417][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:11.418][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:11.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.421][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:11.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.424][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:11.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:11.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.428][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.429][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-01 16:02:11.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.431][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:11.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:11.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.436][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.438][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:11.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:11.439][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.440][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-01 16:02:11.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:11.442][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.443][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.444][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-01 16:02:11.444][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-01 16:02:11.444][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-01 16:02:11.444][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-01 16:02:11.444][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-01 16:02:11.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:11.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:11.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.450][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:11.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:11.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.454][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.455][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-01 16:02:11.456][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.457][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-01 16:02:11.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.459][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:11.460][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.463][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.463][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-01 16:02:11.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:11.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.466][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-01 16:02:11.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:11.468][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.468][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.469][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.470][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:11.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.472][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:11.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.475][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:11.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:11.478][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.482][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.483][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-01 16:02:11.485][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.485][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-01 16:02:11.486][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.487][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:11.488][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.489][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.489][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.491][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-01 16:02:11.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:11.493][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.494][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-01 16:02:11.494][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:11.495][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.496][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.497][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-01 16:02:11.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:11.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.503][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:11.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:11.505][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.506][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.507][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:11.508][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.524][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[2025-11-01 16:02:11.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.542][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[2025-11-01 16:02:11.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.555][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[2025-11-01 16:02:11.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.559][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[2025-11-01 16:02:11.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.566][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-01 16:02:11.567][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-01 16:02:11.569][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-01 16:02:11.570][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-01 16:02:11.571][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-01 16:02:11.576][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-01 16:02:11.577][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:11.578][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:11.579][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-01 16:02:11.580][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-01 16:02:11.581][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-01 16:02:11.582][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-01 16:02:11.583][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-01 16:02:11.584][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-01 16:02:11.585][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-01 16:02:11.586][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-01 16:02:11.587][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-01 16:02:11.588][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-01 16:02:11.589][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-01 16:02:11.590][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-01 16:02:11.591][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-01 16:02:11.592][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-01 16:02:11.593][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-01 16:02:11.594][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-01 16:02:11.595][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-01 16:02:11.596][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-01 16:02:11.597][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-01 16:02:11.598][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-01 16:02:11.599][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-01 16:02:11.600][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-01 16:02:11.601][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-01 16:02:11.602][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-01 16:02:11.603][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-01 16:02:11.604][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-01 16:02:11.605][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-01 16:02:11.606][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-01 16:02:11.607][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-01 16:02:11.608][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-01 16:02:11.609][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-01 16:02:11.610][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-01 16:02:11.611][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-01 16:02:11.612][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-01 16:02:11.613][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-01 16:02:11.614][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-01 16:02:11.615][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-01 16:02:11.616][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-01 16:02:11.617][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-01 16:02:11.618][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-01 16:02:11.619][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-01 16:02:11.620][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-01 16:02:11.621][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-01 16:02:11.622][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-01 16:02:11.623][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-01 16:02:11.624][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-01 16:02:11.625][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-01 16:02:11.626][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-01 16:02:11.627][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-01 16:02:11.628][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-01 16:02:11.629][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-01 16:02:11.630][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-01 16:02:11.631][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-01 16:02:11.632][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-01 16:02:11.633][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-01 16:02:11.634][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-01 16:02:11.635][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-01 16:02:11.636][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-01 16:02:11.637][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-01 16:02:11.638][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-01 16:02:11.639][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-01 16:02:11.640][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-01 16:02:11.641][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-01 16:02:11.642][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-01 16:02:11.643][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-01 16:02:11.644][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-01 16:02:11.645][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-01 16:02:11.646][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-01 16:02:11.647][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-01 16:02:11.648][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-01 16:02:11.649][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-01 16:02:11.650][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-01 16:02:11.651][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-01 16:02:11.652][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-01 16:02:11.653][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-01 16:02:11.654][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-01 16:02:11.656][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-01 16:02:11.661][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-01 16:02:11.662][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.663][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.725][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[2025-11-01 16:02:11.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-01 16:02:11.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-01 16:02:11.741][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-11-01 16:02:11.742][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-11-01 16:02:11.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.745][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-11-01 16:02:11.749][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.750][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-01 16:02:11.751][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.752][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-11-01 16:02:11.752][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.753][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.754][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-11-01 16:02:11.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-01 16:02:11.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.756][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-11-01 16:02:11.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-11-01 16:02:11.758][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-01 16:02:11.759][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.760][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-01 16:02:11.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.762][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-01 16:02:11.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-01 16:02:11.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-01 16:02:11.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-01 16:02:11.765][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:11.765][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-11-01 16:02:11.765][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-11-01 16:02:11.765][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-11-01 16:02:11.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-01 16:02:11.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-01 16:02:11.767][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-01 16:02:11.768][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-01 16:02:11.769][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-11-01 16:02:11.771][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-11-01 16:02:11.775][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-11-01 16:02:11.775][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-01 16:02:11.776][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-11-01 16:02:11.777][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-01 16:02:11.778][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-01 16:02:11.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-01 16:02:11.779][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-01 16:02:11.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-01 16:02:11.780][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-01 16:02:11.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  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
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

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