Back to Long Tests report for BioC 3.21

This page was generated on 2025-08-30 23:55 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
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 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-30 09:55 -0400 (Sat, 30 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-08-30 16:01:16 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 16:35:20 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 2043.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-08-30 16:02:27.527][biodb::testContext]
biodb.INFO [2025-08-30 16:02:27.531][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:02:27.532][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-30 16:02:27.533][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:02:27.534][biodb::testContext]
biodb.INFO [2025-08-30 16:02:27.541][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-30 16:02:27.543][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-30 16:02:27.550][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:27.552][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-30 16:02:27.553][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.558][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-30 16:02:27.582][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.587][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-30 16:02:27.588][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.593][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-30 16:02:27.594][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-30 16:02:27.595][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-30 16:02:27.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.600][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-30 16:02:27.601][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-30 16:02:27.602][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.607][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-30 16:02:27.608][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-30 16:02:27.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.613][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-30 16:02:27.614][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-30 16:02:27.615][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-30 16:02:27.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.620][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-30 16:02:27.621][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.624][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[2025-08-30 16:02:27.626][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-30 16:02:27.627][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-30 16:02:27.628][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-30 16:02:27.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.633][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:02:27.634][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-30 16:02:27.635][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-30 16:02:27.636][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-30 16:02:27.638][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-30 16:02:27.639][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-30 16:02:27.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.643][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-30 16:02:27.645][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-30 16:02:27.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.649][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-30 16:02:27.651][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-30 16:02:27.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.655][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-30 16:02:27.656][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-30 16:02:27.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.661][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-30 16:02:27.662][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-30 16:02:27.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.667][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-30 16:02:27.668][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-30 16:02:27.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.673][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:02:27.674][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-30 16:02:27.685][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-30 16:02:27.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.690][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-30 16:02:27.691][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-30 16:02:27.692][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-30 16:02:27.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.700][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-30 16:02:27.751][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.773][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-30 16:02:27.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.776][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:27.777][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.782][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:02:27.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:27.784][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.786][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-30 16:02:27.787][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:27.788][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.791][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:02:27.791][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:02:27.791][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:02:27.791][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:02:27.791][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:02:27.792][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:27.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.796][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:27.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.800][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.801][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:27.803][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:27.804][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.806][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.807][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-30 16:02:27.809][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.811][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:02:27.812][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.813][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:27.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.817][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.820][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:02:27.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:27.822][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.823][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-30 16:02:27.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:27.826][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.827][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.829][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:02:27.829][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:02:27.829][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:02:27.829][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:02:27.829][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:02:27.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:27.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.834][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:27.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.838][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:27.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:27.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.843][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.845][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-30 16:02:27.847][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.848][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-30 16:02:27.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:27.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.855][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.857][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:02:27.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:27.860][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.861][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-30 16:02:27.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:27.863][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.865][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.866][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:27.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.871][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:27.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.876][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:27.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:27.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.881][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.882][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-30 16:02:27.884][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.885][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:02:27.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:27.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:02:27.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:27.897][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.898][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-30 16:02:27.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:27.901][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.902][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:27.903][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.905][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:02:27.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.908][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:27.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:27.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:27.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:27.913][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.914][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:27.915][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:27.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:27.918][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:27.922][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:27.923][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:27.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:27.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:27.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:27.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:27.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.026][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-30 16:02:28.031][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-30 16:02:28.033][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-30 16:02:28.035][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-30 16:02:28.036][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-30 16:02:28.038][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-30 16:02:28.040][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-30 16:02:28.042][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-30 16:02:28.044][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-30 16:02:28.045][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-30 16:02:28.047][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-30 16:02:28.049][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-30 16:02:28.051][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-30 16:02:28.053][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-30 16:02:28.054][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-30 16:02:28.056][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-30 16:02:28.058][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-30 16:02:28.060][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-30 16:02:28.062][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-30 16:02:28.064][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-30 16:02:28.065][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-30 16:02:28.067][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-30 16:02:28.069][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-30 16:02:28.071][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-30 16:02:28.073][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-30 16:02:28.075][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-30 16:02:28.077][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-30 16:02:28.079][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-30 16:02:28.080][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-30 16:02:28.082][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-30 16:02:28.084][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-30 16:02:28.086][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-30 16:02:28.087][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-30 16:02:28.089][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-30 16:02:28.091][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-30 16:02:28.092][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-30 16:02:28.094][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-30 16:02:28.096][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-30 16:02:28.097][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-30 16:02:28.099][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-30 16:02:28.102][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-30 16:02:28.104][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-30 16:02:28.106][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-30 16:02:28.108][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-30 16:02:28.109][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-30 16:02:28.111][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-30 16:02:28.113][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-30 16:02:28.114][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-30 16:02:28.116][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-30 16:02:28.118][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-30 16:02:28.120][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-30 16:02:28.121][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-30 16:02:28.123][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-30 16:02:28.125][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-30 16:02:28.126][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-30 16:02:28.128][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-30 16:02:28.130][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-30 16:02:28.132][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-30 16:02:28.133][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-30 16:02:28.135][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-30 16:02:28.137][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-30 16:02:28.138][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-30 16:02:28.140][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-30 16:02:28.142][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-30 16:02:28.144][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-30 16:02:28.145][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-30 16:02:28.147][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-30 16:02:28.149][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-30 16:02:28.150][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-30 16:02:28.152][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-30 16:02:28.154][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-30 16:02:28.156][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-30 16:02:28.157][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-30 16:02:28.159][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-30 16:02:28.161][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-30 16:02:28.162][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-30 16:02:28.164][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-30 16:02:28.166][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-30 16:02:28.168][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-30 16:02:28.169][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-30 16:02:28.171][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-30 16:02:28.173][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-30 16:02:28.174][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-30 16:02:28.182][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-30 16:02:28.184][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-30 16:02:28.187][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:02:28.188][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.191][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.313][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[2025-08-30 16:02:28.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:02:28.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:02:28.348][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-30 16:02:28.361][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-30 16:02:28.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:28.365][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-30 16:02:28.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:28.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:02:28.368][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:28.370][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-30 16:02:28.371][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:28.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:02:28.373][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-30 16:02:28.375][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:02:28.376][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:28.377][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-30 16:02:28.378][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-30 16:02:28.380][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-30 16:02:28.381][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-30 16:02:28.382][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:28.383][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-30 16:02:28.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:28.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:28.387][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:02:28.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:02:28.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:02:28.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:02:28.392][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-30 16:02:28.392][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-30 16:02:28.392][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-30 16:02:28.392][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-30 16:02:28.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:02:28.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:02:28.395][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-30 16:02:28.397][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:02:28.405][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-30 16:02:28.426][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-30 16:02:28.428][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-08-30 16:02:28.432][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-08-30 16:02:28.463][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-08-30 16:02:28.467][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-30 16:02:28.469][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-30 16:02:28.470][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:02:28.472][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:02:28.473][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:02:28.475][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-30 16:02:28.484][biodb::testThat]
biodb.INFO [2025-08-30 16:02:28.486][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-30 16:02:28.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:28.488][biodb::testThat]
biodb.TRACE[2025-08-30 16:02:28.492][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-08-30 16:02:28.494][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-30 16:02:28.497][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-30 16:02:28.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-30 16:02:28.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:28.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:28.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:28.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:28.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:28.527][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.TRACE[2025-08-30 16:02:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.620][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:28.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:28.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:28.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:28.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:28.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:28.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:28.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.660][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.675][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:02:28.762][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-08-30 16:02:28.765][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:28.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:28.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.770][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:28.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:28.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:28.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:28.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.871][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.876][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.881][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:28.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.910][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.911][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.913][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:28.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:28.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.945][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.946][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.948][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:28.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:28.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.980][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.981][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.015][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.016][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.050][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.052][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.075][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.076][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.078][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.085][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.096][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.109][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.115][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.117][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.143][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-08-30 16:02:29.192][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-30 16:02:29.194][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-30 16:02:29.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-30 16:02:29.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:02:29.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:02:29.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:02:29.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:02:29.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:02:29.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-30 16:02:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.269][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.362][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:02:29.408][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-08-30 16:02:29.439][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:29.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:29.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:02:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:02:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:29.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-30 16:02:29.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:29.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-30 16:02:29.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.470][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.513][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.523][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:02:29.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.564][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.568][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.584][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.595][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.600][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.601][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.604][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.640][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.644][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.666][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.676][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.678][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.680][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.712][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.713][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.751][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.782][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.786][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.805][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:02:29.807][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:02:29.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.809][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.815][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.816][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:02:29.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.819][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.825][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:02:29.826][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:02:29.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.834][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:02:29.835][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:02:29.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.838][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.844][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.845][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:02:29.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.853][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.855][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:02:29.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.857][ef$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:02:29.863][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:02:29.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:02:29.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:02:29.866][ef$get] fields variable is a list.
biodb.INFO [2025-08-30 16:02:29.876][biodb::testThat]
biodb.INFO [2025-08-30 16:02:29.877][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-30 16:02:29.878][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:02:29.880][biodb::testThat]
biodb.DEBUG[2025-08-30 16:02:29.882][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-08-30 16:02:29.889][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-08-30 16:02:29.893][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-08-30 16:02:29.895][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-08-30 16:02:29.896][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-08-30 16:02:29.898][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-08-30 16:02:29.900][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-08-30 16:02:36.564][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus106f57233762agz".
biodb.TRACE[2025-08-30 16:02:36.565][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-30 16:02:36.567][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-30 16:02:36.568][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-30 16:02:36.570][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-08-30 16:02:36.572][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker106f51092f9f9marker".
biodb.TRACE[2025-08-30 16:02:36.578][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-08-30 16:02:36.579][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-30 16:02:36.581][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-30 16:02:36.583][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-30 16:02:36.584][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-08-30 16:02:36.586][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-08-30 16:03:59.430][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-08-30 16:03:59.433][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-08-30 16:32:49.726][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-08-30 16:32:50.315][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-08-30 16:35:15.703][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-08-30 16:35:15.705][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-08-30 16:35:17.184][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker106f5215952efmarker".
biodb.TRACE[2025-08-30 16:35:17.186][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-08-30 16:35:17.188][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-08-30 16:35:17.190][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-08-30 16:35:17.192][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-08-30 16:35:17.195][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-08-30 16:35:17.196][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-08-30 16:35:17.199][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-08-30 16:35:17.201][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-08-30 16:35:17.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-30 16:35:17.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:17.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:17.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:17.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:17.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:17.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-30 16:35:17.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:35:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:35:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:35:17.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:35:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:35:17.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:35:17.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:35:17.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:35:17.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.304][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.309][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:35:17.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-30 16:35:17.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:17.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:17.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:17.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:17.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:17.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-30 16:35:17.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.390][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:35:17.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:35:17.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.396][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-30 16:35:17.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-30 16:35:17.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:35:17.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:35:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-30 16:35:17.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-30 16:35:17.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-30 16:35:17.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-30 16:35:17.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-30 16:35:17.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:35:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:35:17.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-30 16:35:17.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-30 16:35:17.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-30 16:35:17.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.497][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.503][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.516][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-30 16:35:17.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-30 16:35:17.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-30 16:35:17.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-30 16:35:17.582][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-08-30 16:35:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-30 16:35:17.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-30 16:35:17.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-30 16:35:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-30 16:35:17.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-30 16:35:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-30 16:35:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-30 16:35:17.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-30 16:35:17.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-30 16:35:17.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-30 16:35:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-30 16:35:17.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-30 16:35:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-30 16:35:17.640][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.641][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-30 16:35:17.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.644][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.653][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.654][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-30 16:35:17.656][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.657][biodb::testThat]
biodb.WARN [2025-08-30 16:35:17.691][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-30 16:35:17.723][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-30 16:35:17.736][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.737][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-30 16:35:17.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.740][biodb::testThat]
biodb.TRACE[2025-08-30 16:35:17.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-30 16:35:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-30 16:35:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-30 16:35:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-30 16:35:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-30 16:35:17.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-30 16:35:17.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-30 16:35:17.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-30 16:35:17.881][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-30 16:35:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-30 16:35:17.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-30 16:35:17.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-30 16:35:17.896][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.898][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-30 16:35:17.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.900][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.911][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.913][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-30 16:35:17.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.916][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.926][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.928][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-30 16:35:17.929][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.931][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.940][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.942][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-30 16:35:17.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-30 16:35:17.945][biodb::testThat]
biodb.INFO [2025-08-30 16:35:17.954][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-30 16:35:17.955][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-08-30 16:35:17.957][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-30 16:35:17.958][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-30 16:35:17.960][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:17.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:17.962][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:17.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:17.965][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:17.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-30 16:35:17.983][biodb::testContext]
biodb.INFO [2025-08-30 16:35:17.985][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:35:17.986][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-08-30 16:35:17.988][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-30 16:35:17.989][biodb::testContext]
biodb.INFO [2025-08-30 16:35:17.994][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-30 16:35:17.997][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-30 16:35:18.003][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:35:18.004][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-30 16:35:18.006][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.011][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-30 16:35:18.013][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.018][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-30 16:35:18.020][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.025][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-30 16:35:18.027][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-30 16:35:18.028][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-30 16:35:18.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.034][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-30 16:35:18.035][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-30 16:35:18.037][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.042][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-30 16:35:18.044][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-30 16:35:18.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.049][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-30 16:35:18.050][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-30 16:35:18.052][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-30 16:35:18.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.057][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-30 16:35:18.059][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.064][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-30 16:35:18.066][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-30 16:35:18.067][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-30 16:35:18.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.072][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:35:18.074][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-30 16:35:18.075][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-30 16:35:18.077][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-30 16:35:18.078][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-30 16:35:18.080][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-30 16:35:18.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.085][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-30 16:35:18.086][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-30 16:35:18.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.092][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-30 16:35:18.093][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-30 16:35:18.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.099][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-30 16:35:18.100][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-30 16:35:18.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.105][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-30 16:35:18.107][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-30 16:35:18.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.112][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-30 16:35:18.114][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-30 16:35:18.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.119][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-30 16:35:18.121][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-30 16:35:18.145][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-30 16:35:18.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.150][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-30 16:35:18.152][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-30 16:35:18.153][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-30 16:35:18.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.160][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-30 16:35:18.163][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.165][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-30 16:35:18.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:35:18.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.172][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.175][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:35:18.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:35:18.178][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.179][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-30 16:35:18.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:35:18.182][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:35:18.185][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:35:18.185][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:35:18.185][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:35:18.185][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:35:18.187][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:35:18.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.191][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:35:18.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.197][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.198][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:35:18.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:35:18.201][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.202][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.204][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-30 16:35:18.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.208][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:35:18.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:35:18.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.218][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:35:18.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:35:18.221][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.223][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-30 16:35:18.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:35:18.226][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.229][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-30 16:35:18.229][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-30 16:35:18.229][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-30 16:35:18.229][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-30 16:35:18.229][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-30 16:35:18.230][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:35:18.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:35:18.236][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.237][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.238][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.240][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.241][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:35:18.243][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:35:18.244][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.245][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.247][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-30 16:35:18.250][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.251][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-30 16:35:18.253][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.254][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:35:18.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.259][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.260][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.262][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-30 16:35:18.263][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:35:18.265][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.266][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-30 16:35:18.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:35:18.269][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.271][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.272][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:35:18.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.278][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:35:18.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.284][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:35:18.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:35:18.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.292][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-30 16:35:18.295][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.297][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-30 16:35:18.299][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:35:18.302][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.307][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.308][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-30 16:35:18.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:35:18.312][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.313][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-30 16:35:18.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:35:18.317][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.318][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.320][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.321][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-30 16:35:18.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:35:18.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.330][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.332][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.334][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:35:18.335][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:35:18.337][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.339][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.341][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:35:18.343][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.344][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[2025-08-30 16:35:18.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.467][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-30 16:35:18.470][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-30 16:35:18.472][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-30 16:35:18.474][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-30 16:35:18.476][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-30 16:35:18.478][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-30 16:35:18.480][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-30 16:35:18.482][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-30 16:35:18.484][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-30 16:35:18.487][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-30 16:35:18.489][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-30 16:35:18.491][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-30 16:35:18.493][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-30 16:35:18.495][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-30 16:35:18.497][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-30 16:35:18.500][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-30 16:35:18.502][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-30 16:35:18.504][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-30 16:35:18.506][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-30 16:35:18.508][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-30 16:35:18.511][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-30 16:35:18.513][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-30 16:35:18.515][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-30 16:35:18.517][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-30 16:35:18.519][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-30 16:35:18.522][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-30 16:35:18.524][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-30 16:35:18.526][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-30 16:35:18.528][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-30 16:35:18.530][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-30 16:35:18.533][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-30 16:35:18.535][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-30 16:35:18.537][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-30 16:35:18.539][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-30 16:35:18.541][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-30 16:35:18.544][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-30 16:35:18.546][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-30 16:35:18.548][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-30 16:35:18.550][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-30 16:35:18.552][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-30 16:35:18.554][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-30 16:35:18.557][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-30 16:35:18.559][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-30 16:35:18.561][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-30 16:35:18.563][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-30 16:35:18.565][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-30 16:35:18.567][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-30 16:35:18.569][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-30 16:35:18.572][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-30 16:35:18.574][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-30 16:35:18.576][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-30 16:35:18.578][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-30 16:35:18.581][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-30 16:35:18.583][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-30 16:35:18.585][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-30 16:35:18.587][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-30 16:35:18.589][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-30 16:35:18.592][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-30 16:35:18.594][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-30 16:35:18.596][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-30 16:35:18.598][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-30 16:35:18.600][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-30 16:35:18.603][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-30 16:35:18.605][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-30 16:35:18.607][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-30 16:35:18.609][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-30 16:35:18.611][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-30 16:35:18.614][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-30 16:35:18.616][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-30 16:35:18.618][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-30 16:35:18.620][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-30 16:35:18.622][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-30 16:35:18.625][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-30 16:35:18.627][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-30 16:35:18.629][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-30 16:35:18.631][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-30 16:35:18.633][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-30 16:35:18.636][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-30 16:35:18.638][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-30 16:35:18.640][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-30 16:35:18.642][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-30 16:35:18.644][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-30 16:35:18.647][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-30 16:35:18.649][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-30 16:35:18.651][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-30 16:35:18.653][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-30 16:35:18.655][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.657][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.795][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[2025-08-30 16:35:18.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-30 16:35:18.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-30 16:35:18.828][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-30 16:35:18.832][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-30 16:35:18.836][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.838][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-30 16:35:18.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.842][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-30 16:35:18.844][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.845][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-30 16:35:18.847][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.851][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-30 16:35:18.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-30 16:35:18.854][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.855][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-30 16:35:18.857][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-30 16:35:18.858][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-30 16:35:18.860][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-30 16:35:18.861][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.863][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-30 16:35:18.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-30 16:35:18.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-30 16:35:18.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-30 16:35:18.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-30 16:35:18.872][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-30 16:35:18.872][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-30 16:35:18.872][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-30 16:35:18.872][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-30 16:35:18.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-30 16:35:18.875][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-30 16:35:18.877][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-30 16:35:18.878][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-30 16:35:18.880][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-30 16:35:18.886][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-30 16:35:18.887][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-08-30 16:35:18.890][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-08-30 16:35:18.892][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-08-30 16:35:18.894][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-30 16:35:18.895][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-30 16:35:18.897][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:35:18.899][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:35:18.901][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-08-30 16:35:18.902][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-30 16:35:18.904][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-30 16:35:18.905][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-08-30 16:35:18.907][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-30 16:35:18.908][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-30 16:35:18.909][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-30 16:35:18.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-30 16:35:18.912][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-30 16:35:18.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-30 16:35:18.915][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-30 16:35:18.916][FUN] Functions in observer 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 0 | WARN 5 | SKIP 0 | PASS 92 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1220.906  264.972 1973.623

'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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.12.0’
* 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.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 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’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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-3.21-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)