Back to Long Tests report for BioC 3.21

This page was generated on 2025-02-01 23:55 -0500 (Sat, 01 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
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 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-02-01 09:55 -0500 (Sat, 01 Feb 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 10e1a05
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway

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

raw results


Summary

Package: biodbNci
Version: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2025-02-01 16:01:04 -0500 (Sat, 01 Feb 2025)
EndedAt: 2025-02-01 16:23:48 -0500 (Sat, 01 Feb 2025)
EllapsedTime: 1363.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-02-01 16:01:53.617][biodb::testContext]
biodb.INFO [2025-02-01 16:01:53.619][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-01 16:01:53.620][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-02-01 16:01:53.621][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-01 16:01:53.621][biodb::testContext]
biodb.INFO [2025-02-01 16:01:53.625][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-01 16:01:53.627][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-01 16:01:53.632][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:01:53.633][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-01 16:01:53.634][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.637][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-01 16:01:53.649][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-01 16:01:53.653][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.656][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-01 16:01:53.656][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-01 16:01:53.657][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-01 16:01:53.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.659][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[2025-02-01 16:01:53.660][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-01 16:01:53.660][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-01 16:01:53.661][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.664][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-01 16:01:53.664][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-01 16:01:53.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.666][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[2025-02-01 16:01:53.667][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-01 16:01:53.668][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-01 16:01:53.668][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-01 16:01:53.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.671][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-01 16:01:53.672][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.674][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-01 16:01:53.675][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-01 16:01:53.676][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-01 16:01:53.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.678][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-01 16:01:53.679][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-01 16:01:53.680][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-01 16:01:53.680][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-01 16:01:53.681][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-01 16:01:53.682][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-01 16:01:53.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.684][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-01 16:01:53.685][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-01 16:01:53.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.688][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-01 16:01:53.689][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-01 16:01:53.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.691][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-01 16:01:53.692][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-01 16:01:53.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.694][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-01 16:01:53.695][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-01 16:01:53.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.698][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-01 16:01:53.698][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-01 16:01:53.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.701][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-01 16:01:53.702][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-01 16:01:53.717][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-01 16:01:53.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.719][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[2025-02-01 16:01:53.720][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-01 16:01:53.720][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-01 16:01:53.721][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-01 16:01:53.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.726][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-01 16:01:53.748][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.764][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-01 16:01:53.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:01:53.766][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.767][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.768][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-01 16:01:53.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:01:53.770][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.771][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-01 16:01:53.772][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:01:53.772][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-01 16:01:53.774][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:01:53.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.776][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:01:53.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.778][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.779][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:01:53.780][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:01:53.781][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.782][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.783][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-01 16:01:53.784][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.784][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-01 16:01:53.785][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:01:53.787][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.788][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.789][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.789][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-01 16:01:53.790][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:01:53.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.791][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-01 16:01:53.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:01:53.793][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-01 16:01:53.794][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-01 16:01:53.795][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:01:53.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:01:53.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.799][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.800][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.800][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:01:53.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:01:53.802][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.802][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.803][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-01 16:01:53.804][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.805][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-01 16:01:53.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:01:53.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.809][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.810][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-01 16:01:53.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:01:53.812][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.812][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-01 16:01:53.813][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:01:53.814][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.815][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:01:53.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.818][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:01:53.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.820][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.820][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:01:53.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:01:53.822][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.823][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.824][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-01 16:01:53.825][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.826][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-01 16:01:53.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:01:53.828][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.829][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.830][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.831][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-01 16:01:53.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:01:53.832][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.833][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-01 16:01:53.834][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:01:53.834][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.835][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:53.836][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:01:53.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.839][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:01:53.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:53.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:53.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:01:53.841][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.842][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:01:53.843][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:01:53.843][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:53.844][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:53.847][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:01:53.847][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:53.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:53.907][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-01 16:01:53.909][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-01 16:01:53.911][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-01 16:01:53.912][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-01 16:01:53.913][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-01 16:01:53.914][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-01 16:01:53.915][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-01 16:01:53.916][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-01 16:01:53.917][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-01 16:01:53.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-01 16:01:53.919][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-01 16:01:53.920][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-01 16:01:53.921][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-01 16:01:53.922][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-01 16:01:53.922][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-01 16:01:53.923][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-01 16:01:53.924][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-01 16:01:53.925][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-01 16:01:53.926][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-01 16:01:53.927][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-01 16:01:53.928][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-01 16:01:53.929][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-01 16:01:53.930][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-01 16:01:53.931][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-01 16:01:53.932][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-01 16:01:53.933][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-01 16:01:53.934][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-01 16:01:53.935][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-01 16:01:53.936][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-01 16:01:53.937][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-01 16:01:53.938][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-01 16:01:53.939][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-01 16:01:53.940][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-01 16:01:53.941][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-01 16:01:53.942][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-01 16:01:53.943][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-01 16:01:53.944][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-01 16:01:53.945][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-01 16:01:53.946][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-01 16:01:53.947][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-01 16:01:53.948][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-01 16:01:53.949][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-01 16:01:53.950][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-01 16:01:53.951][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-01 16:01:53.952][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-01 16:01:53.953][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-01 16:01:53.954][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-01 16:01:53.955][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-01 16:01:53.956][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-01 16:01:53.957][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-01 16:01:53.958][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-01 16:01:53.959][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-01 16:01:53.960][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-01 16:01:53.961][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-01 16:01:53.962][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-01 16:01:53.962][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-01 16:01:53.963][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-01 16:01:53.964][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-01 16:01:53.965][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-01 16:01:53.966][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-01 16:01:53.967][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-01 16:01:53.968][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-01 16:01:53.969][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-01 16:01:53.970][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-01 16:01:53.971][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-01 16:01:53.972][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-01 16:01:53.973][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-01 16:01:53.974][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-01 16:01:53.975][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-01 16:01:53.976][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-01 16:01:53.977][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-01 16:01:53.978][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-01 16:01:53.979][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-01 16:01:53.980][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-01 16:01:53.981][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-01 16:01:53.982][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-01 16:01:53.983][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-01 16:01:53.984][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-01 16:01:53.985][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-01 16:01:53.986][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-01 16:01:53.987][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-01 16:01:53.988][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-01 16:01:53.989][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-01 16:01:53.993][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-01 16:01:53.994][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-01 16:01:53.996][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:01:53.997][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:53.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:53.998][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:53.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.025][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[2025-02-01 16:01:54.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:01:54.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:01:54.083][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-01 16:01:54.090][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-01 16:01:54.091][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:54.092][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-01 16:01:54.092][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:54.093][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:01:54.094][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:54.094][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-01 16:01:54.095][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:54.096][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:01:54.097][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-01 16:01:54.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:01:54.098][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:54.099][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-01 16:01:54.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-01 16:01:54.100][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-01 16:01:54.101][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-01 16:01:54.101][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:54.102][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-01 16:01:54.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:54.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:54.104][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:01:54.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:01:54.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:01:54.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:01:54.107][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-01 16:01:54.107][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-01 16:01:54.107][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-01 16:01:54.107][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-01 16:01:54.108][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:01:54.108][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:01:54.109][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-01 16:01:54.110][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:01:54.114][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-01 16:01:54.130][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-01 16:01:54.131][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-01 16:01:54.134][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-01 16:01:54.136][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-01 16:01:54.139][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-01 16:01:54.140][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-01 16:01:54.141][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:01:54.142][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:01:54.143][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:01:54.143][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-01 16:01:54.177][biodb::testThat]
biodb.INFO [2025-02-01 16:01:54.178][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-01 16:01:54.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:01:54.180][biodb::testThat]
biodb.TRACE[2025-02-01 16:01:54.182][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[2025-02-01 16:01:54.183][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-01 16:01:54.185][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-01 16:01:54.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-01 16:01:54.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.203][FUN] Functions in observer BiodbConfig: [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[2025-02-01 16:01:54.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.271][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.274][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.280][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-01 16:01:54.327][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-02-01 16:01:54.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-01 16:01:54.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-01 16:01:54.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-01 16:01:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-01 16:01:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.364][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.416][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.417][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.419][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.434][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.437][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.438][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.440][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.458][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.459][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.460][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.479][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.479][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.481][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.496][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.500][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.501][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.511][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.512][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.514][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.522][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.523][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.528][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.529][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.530][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.534][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.536][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.540][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.541][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.542][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.555][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[2025-02-01 16:01:54.579][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-01 16:01:54.580][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-01 16:01:54.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-01 16:01:54.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:01:54.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:01:54.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:01:54.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:01:54.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:01:54.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-01 16:01:54.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.620][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.669][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.671][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.677][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-01 16:01:54.697][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-02-01 16:01:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.714][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:01:54.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-01 16:01:54.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-01 16:01:54.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.724][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-01 16:01:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-01 16:01:54.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.760][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.763][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.765][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:01:54.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.790][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.792][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.802][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.805][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.808][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.811][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.812][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.813][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.832][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.838][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.851][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.856][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.858][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.877][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.878][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.879][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.899][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.900][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.919][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.920][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.921][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.932][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:01:54.932][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:01:54.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.934][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.938][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.939][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:01:54.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.940][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.944][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:01:54.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:01:54.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.946][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:01:54.955][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:01:54.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.956][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:01:54.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.962][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.966][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.967][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:01:54.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.969][ef$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:01:54.972][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:01:54.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:01:54.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:01:54.974][ef$get] fields variable is a list.
biodb.INFO [2025-02-01 16:01:54.981][biodb::testThat]
biodb.INFO [2025-02-01 16:01:54.982][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-01 16:01:54.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:01:54.984][biodb::testThat]
biodb.DEBUG[2025-02-01 16:01:54.985][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-02-01 16:01:54.990][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-02-01 16:01:54.994][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-02-01 16:01:54.994][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-02-01 16:01:54.995][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-02-01 16:01:54.996][sched$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[2025-02-01 16:02:26.764][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactusdde4511d1d06gz".
biodb.TRACE[2025-02-01 16:02:26.765][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-01 16:02:26.766][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-01 16:02:26.767][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-01 16:02:26.768][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-02-01 16:02:26.769][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerdde44e5c9e84marker".
biodb.TRACE[2025-02-01 16:02:26.770][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-02-01 16:02:26.771][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-01 16:02:26.772][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-02-01 16:02:26.773][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-02-01 16:02:26.774][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-02-01 16:02:26.775][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-01 16:03:23.359][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-02-01 16:03:23.361][private$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[2025-02-01 16:22:29.049][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-02-01 16:22:29.386][private$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[2025-02-01 16:23:35.543][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-01 16:23:35.545][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-02-01 16:23:35.548][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerdde422ab144dmarker".
biodb.TRACE[2025-02-01 16:23:35.549][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-02-01 16:23:35.550][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-02-01 16:23:35.552][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-02-01 16:23:35.553][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-02-01 16:23:35.583][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-02-01 16:23:36.202][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-02-01 16:23:36.204][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-02-01 16:23:36.205][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-02-01 16:23:36.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-01 16:23:36.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:36.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:36.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:36.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:36.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:36.268][FUN] Functions in observer BiodbConfig: [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[2025-02-01 16:23:36.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:23:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:23:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:23:36.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:23:36.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:23:36.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:23:36.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:23:36.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:23:36.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.309][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.312][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.319][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-01 16:23:36.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-01 16:23:36.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:36.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:36.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:36.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:36.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:36.340][FUN] Functions in observer BiodbConfig: [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[2025-02-01 16:23:36.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.355][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:23:36.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:23:36.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.358][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-01 16:23:36.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-01 16:23:36.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:23:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:23:36.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-01 16:23:36.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-01 16:23:36.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-01 16:23:36.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-01 16:23:36.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-01 16:23:36.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:23:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:23:36.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-01 16:23:36.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-01 16:23:36.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-01 16:23:36.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.412][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.416][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.422][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-01 16:23:36.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-01 16:23:36.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-01 16:23:36.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-01 16:23:36.454][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-02-01 16:23:36.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-01 16:23:36.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-01 16:23:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-01 16:23:36.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-01 16:23:36.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-01 16:23:36.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-01 16:23:36.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-01 16:23:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-01 16:23:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-01 16:23:36.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-01 16:23:36.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-01 16:23:36.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-01 16:23:36.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-01 16:23:36.488][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.490][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-01 16:23:36.490][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.491][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.497][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.498][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-01 16:23:36.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.499][biodb::testThat]
biodb.WARN [2025-02-01 16:23:36.517][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-02-01 16:23:36.532][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-02-01 16:23:36.540][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.541][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-01 16:23:36.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.543][biodb::testThat]
biodb.TRACE[2025-02-01 16:23:36.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.704][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-01 16:23:36.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-01 16:23:36.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.712][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-01 16:23:36.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-01 16:23:36.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-01 16:23:36.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-01 16:23:36.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-01 16:23:36.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-01 16:23:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-01 16:23:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-01 16:23:36.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-01 16:23:36.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-01 16:23:36.904][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.905][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-01 16:23:36.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.907][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.914][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.915][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-01 16:23:36.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.917][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.924][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.925][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-01 16:23:36.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.926][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.932][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.933][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-01 16:23:36.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-01 16:23:36.934][biodb::testThat]
biodb.INFO [2025-02-01 16:23:36.940][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-01 16:23:36.941][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-01 16:23:36.942][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-01 16:23:36.942][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-01 16:23:36.943][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:36.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:36.945][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:36.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:36.946][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:36.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-01 16:23:38.987][biodb::testContext]
biodb.INFO [2025-02-01 16:23:38.988][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-01 16:23:38.989][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-02-01 16:23:38.990][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-01 16:23:38.991][biodb::testContext]
biodb.INFO [2025-02-01 16:23:39.062][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-01 16:23:40.972][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-01 16:23:42.780][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:23:42.783][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-01 16:23:42.784][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.787][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-01 16:23:42.788][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.791][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-01 16:23:42.792][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.795][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-01 16:23:42.796][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-01 16:23:42.797][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-01 16:23:42.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.800][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-01 16:23:42.801][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-01 16:23:42.801][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.804][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[2025-02-01 16:23:42.805][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-01 16:23:42.805][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-01 16:23:42.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.831][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-01 16:23:42.833][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-01 16:23:42.833][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-01 16:23:42.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.837][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-01 16:23:42.838][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.842][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-01 16:23:42.871][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-01 16:23:42.873][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-01 16:23:42.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.876][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-01 16:23:42.877][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-01 16:23:42.878][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-01 16:23:42.879][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-01 16:23:42.880][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-01 16:23:42.881][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-01 16:23:42.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.885][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-01 16:23:42.886][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-01 16:23:42.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.890][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-01 16:23:42.891][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-01 16:23:42.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.894][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-01 16:23:42.895][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-01 16:23:42.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.898][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-01 16:23:42.899][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-01 16:23:42.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.902][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-01 16:23:42.903][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-01 16:23:42.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:42.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:42.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:42.906][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-01 16:23:42.907][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-01 16:23:43.634][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-01 16:23:44.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.758][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-01 16:23:44.759][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-01 16:23:44.769][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-01 16:23:44.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.773][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-01 16:23:44.774][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.775][self$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[2025-02-01 16:23:44.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:23:44.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.781][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-01 16:23:44.782][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:23:44.783][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.783][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-01 16:23:44.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:23:44.785][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.786][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.787][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-01 16:23:44.787][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-01 16:23:44.787][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-01 16:23:44.787][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-01 16:23:44.787][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-01 16:23:44.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:23:44.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:23:44.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.815][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.816][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:23:44.817][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:23:44.818][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.819][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.820][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-01 16:23:44.821][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.822][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-01 16:23:44.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:23:44.824][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.825][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.848][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-01 16:23:44.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:23:44.850][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.851][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-01 16:23:44.851][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:23:44.852][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.853][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-01 16:23:44.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-01 16:23:44.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-01 16:23:44.854][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-01 16:23:44.854][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-01 16:23:44.855][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:23:44.856][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.857][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:23:44.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.859][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.860][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.861][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:23:44.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:23:44.863][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.863][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.864][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-01 16:23:44.866][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.867][self$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[2025-02-01 16:23:44.867][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.868][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:23:44.869][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.870][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.871][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.871][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.872][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-01 16:23:44.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:23:44.874][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.875][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-01 16:23:44.875][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:23:44.876][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.877][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.878][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.879][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:23:44.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.881][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:23:44.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.884][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:23:44.885][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:23:44.886][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.887][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.888][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-01 16:23:44.889][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.890][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-01 16:23:44.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:23:44.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.893][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.896][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-01 16:23:44.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:23:44.898][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.899][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-01 16:23:44.899][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:23:44.900][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:44.902][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.903][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-01 16:23:44.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.905][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:23:44.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:44.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:44.907][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:23:44.908][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:23:44.909][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:23:44.910][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:44.911][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:44.912][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:23:44.913][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.948][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[2025-02-01 16:23:44.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.959][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[2025-02-01 16:23:44.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.966][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.DEBUG[2025-02-01 16:23:44.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:44.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:44.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:44.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:44.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:44.981][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-01 16:23:44.982][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-01 16:23:44.983][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-01 16:23:44.985][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-01 16:23:44.986][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-01 16:23:44.987][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-01 16:23:44.988][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-01 16:23:44.989][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-01 16:23:46.580][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-01 16:23:46.582][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-01 16:23:46.583][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-01 16:23:46.584][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-01 16:23:46.586][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-01 16:23:46.587][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-01 16:23:46.588][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-01 16:23:46.589][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-01 16:23:46.590][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-01 16:23:46.591][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-01 16:23:46.882][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-01 16:23:46.883][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-01 16:23:46.885][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-01 16:23:46.894][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-01 16:23:46.906][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-01 16:23:46.939][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-01 16:23:46.941][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-01 16:23:46.942][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-01 16:23:46.943][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-01 16:23:46.944][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-01 16:23:46.945][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-01 16:23:46.946][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-01 16:23:46.947][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-01 16:23:46.948][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-01 16:23:46.949][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-01 16:23:46.951][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-01 16:23:46.952][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-01 16:23:46.953][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-01 16:23:46.954][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-01 16:23:46.955][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-01 16:23:46.956][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-01 16:23:46.957][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-01 16:23:46.958][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-01 16:23:46.959][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-01 16:23:46.960][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-01 16:23:46.962][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-01 16:23:46.963][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-01 16:23:46.964][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-01 16:23:46.965][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-01 16:23:46.966][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-01 16:23:46.967][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-01 16:23:46.968][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-01 16:23:46.969][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-01 16:23:46.971][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-01 16:23:46.972][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-01 16:23:46.973][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-01 16:23:46.974][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-01 16:23:46.975][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-01 16:23:46.976][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-01 16:23:46.977][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-01 16:23:46.978][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-01 16:23:46.979][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-01 16:23:46.981][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-01 16:23:46.982][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-01 16:23:46.983][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-01 16:23:46.984][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-01 16:23:46.985][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-01 16:23:46.986][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-01 16:23:46.987][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-01 16:23:46.988][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-01 16:23:46.989][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-01 16:23:46.991][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-01 16:23:46.992][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-01 16:23:46.993][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-01 16:23:46.994][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-01 16:23:46.995][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-01 16:23:46.996][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-01 16:23:46.997][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-01 16:23:46.998][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-01 16:23:47.000][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-01 16:23:47.001][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-01 16:23:47.002][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-01 16:23:47.003][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-01 16:23:47.004][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-01 16:23:47.005][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-01 16:23:47.006][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-01 16:23:47.008][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-01 16:23:47.009][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-01 16:23:47.009][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.011][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.017][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[2025-02-01 16:23:47.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.032][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[2025-02-01 16:23:47.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.047][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[2025-02-01 16:23:47.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-01 16:23:47.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-01 16:23:47.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.097][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[2025-02-01 16:23:47.169][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-01 16:23:47.192][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-01 16:23:47.213][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:47.214][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-01 16:23:47.215][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:47.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-01 16:23:47.217][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:47.218][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-01 16:23:47.219][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:47.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-01 16:23:47.220][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-01 16:23:47.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-01 16:23:47.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:47.223][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-01 16:23:47.223][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-01 16:23:47.224][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-01 16:23:47.225][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-01 16:23:47.226][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:47.227][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-01 16:23:47.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:47.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:47.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-01 16:23:47.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-01 16:23:47.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-01 16:23:47.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-01 16:23:47.232][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-01 16:23:47.232][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-01 16:23:47.232][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-01 16:23:47.232][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-01 16:23:47.233][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-01 16:23:47.234][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-01 16:23:47.234][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-01 16:23:47.235][self$setPropertyValue]
biodb.DEBUG[2025-02-01 16:23:47.236][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-01 16:23:47.239][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-01 16:23:47.240][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-01 16:23:47.241][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-01 16:23:47.242][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-01 16:23:47.243][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-01 16:23:47.244][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-01 16:23:47.245][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:23:47.246][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:23:47.247][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-01 16:23:47.248][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-01 16:23:47.248][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-01 16:23:47.249][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-01 16:23:47.250][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-01 16:23:47.251][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-01 16:23:47.252][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-01 16:23:47.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-01 16:23:47.253][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-01 16:23:47.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-01 16:23:47.254][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-01 16:23:47.255][FUN] Functions in observer 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 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1005.073  220.339 1315.086

'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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* 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 ‘1.11.0’
* 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 ‘1.11.0’
** 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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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 -Wl,-framework -Wl,CoreFoundation
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)